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Fornaini NR, Černohorská H, do Vale Martins L, Knytl M. Cytogenetic Analysis of the Fish Genus Carassius Indicates Divergence, Fission, and Segmental Duplication as Drivers of Tandem Repeat and Microchromosome Evolution. Genome Biol Evol 2024; 16:evae028. [PMID: 38340334 DOI: 10.1093/gbe/evae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
Fishes of the genus Carassius are useful experimental vertebrate models for the study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Those Carassius polyploids with ≥150 chromosomes have microchromosomes, but the origin of microchromosomes, especially in European populations, is unknown. We used cytogenetics to study evolution of tandem repeats (U1 and U2 small nuclear DNAs and H3 histone) and microchromosomes in Carassius from the Czech Republic. We tested the hypotheses whether the number of tandem repeats was affected by polyploidization or divergence between species and what mechanism drives evolution of microchromosomes. Tandem repeats were found in tetraploid and hexaploid Carassius gibelio, and tetraploid Carassius auratus and Carassius carassius in conserved numbers, with the exception of U1 small nuclear DNA in C. auratus. This conservation indicates reduction and/or loss in the number of copies per locus in hexaploids and may have occurred by divergence rather than polyploidization. To study the evolution of microchromosomes, we used the whole microchromosome painting probe from hexaploid C. gibelio and hybridized it to tetraploid and hexaploid C. gibelio, and tetraploid C. auratus and C. carassius. Our results revealed variation in the number of microchromosomes in hexaploids and indicated that the evolution of the Carassius karyotype is governed by macrochromosome fissions followed by segmental duplication in pericentromeric areas. These are potential mechanisms responsible for the presence of microchromosomes in Carassius hexaploids. Differential efficacy of one or both of these mechanisms in different tetraploids could ensure variability in chromosome number in polyploids in general.
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Affiliation(s)
- Nicola R Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Halina Černohorská
- Genetics and Reproductive Biotechnologies, CEITEC-Veterinary Research Institute, Brno 62100, Czech Republic
| | | | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12843, Czech Republic
- Department of Biology, McMaster University, Hamilton, Ontario L8S4K1, Canada
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Xu M, Guo H, Wang Y, Zhou B. Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes. Genome 2024; 67:64-77. [PMID: 37922519 DOI: 10.1139/gen-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.
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Affiliation(s)
- Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyue Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Yingying Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production co-sponsored by Jiangsu Province and Ministry of Education, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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Li C, Fu L, Wang Q, Liu H, Chen G, Qi F, Zhang M, Jia Y, Li X, Huang B, Dong W, Du P, Zhang X. Development and application of whole- chromosome painting of chromosomes 7A and 8A of Arachis duranensis based on chromosome-specific single-copy oligonucleotides. Genome 2024. [PMID: 38394647 DOI: 10.1139/gen-2023-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
For peanut, the lack of stable cytological markers is a barrier to tracking specific chromosomes, elucidating the genetic relationships between genomes and identifying chromosomal variations. Chromosome mapping using single-copy oligonucleotide (oligo) probe libraries has unique advantages for identifying homologous chromosomes and chromosomal rearrangements. In this study, we developed two whole-chromosome single-copy oligo probe libraries, LS-7A and LS-8A, based on the reference genome sequences of chromosomes 7A and 8A of Arachis duranensis. Fluorescence in situ hybridization (FISH) analysis confirmed that the libraries could specifically paint chromosomes 7 and 8. In addition, sequential FISH and electronic localization of LS-7A and LS-8A in A. duranensis (AA) and A. ipaensis (BB) showed that chromosomes 7A and 8A contained translocations and inversions relative to chromosomes 7B and 8B. Analysis of the chromosomes of wild Arachis species using LS-8A confirmed that this library could accurately and effectively identify A genome species. Finally, LS-7A and LS-8A were used to paint the chromosomes of interspecific hybrids and their progenies, which verified the authenticity of the interspecific hybrids and identified a disomic addition line. This study provides a model for developing specific oligo probes to identify the structural variations of other chromosomes in Arachis and demonstrates the practical utility of LS-7A and LS-8A.
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Affiliation(s)
- Chenyu Li
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Liuyang Fu
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Qian Wang
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Hua Liu
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Guoquan Chen
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Feiyan Qi
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Maoning Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yaoguang Jia
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaona Li
- College of Life Science, Zhengzhou University, Zhengzhou, Henan 450001, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Bingyan Huang
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Wenzhao Dong
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Pei Du
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Shennong Laboratory/Nation Industrial Innovation Centre for Bio-Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement/Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
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Gokhman VE. Chromosome study of the Hymenoptera (Insecta): from cytogenetics to cytogenomics. Comp Cytogenet 2023; 17:239-250. [PMID: 37953851 PMCID: PMC10632776 DOI: 10.3897/compcytogen.17.112332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023]
Abstract
A brief overview of the current stage of the chromosome study of the insect order Hymenoptera is given. It is demonstrated that, in addition to routine staining and other traditional techniques of chromosome research, karyotypes of an increasing number of hymenopterans are being studied using molecular methods, e.g., staining with base-specific fluorochromes and fluorescence in situ hybridization (FISH), including microdissection and chromosome painting. Due to the advent of whole genome sequencing and other molecular techniques, together with the "big data" approach to the chromosomal data, the current stage of the chromosome research on Hymenoptera represents a transition from Hymenoptera cytogenetics to cytogenomics.
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Affiliation(s)
- Vladimir E. Gokhman
- Botanical Garden, Moscow State University, Moscow 119234, RussiaMoscow State UniversityMoscowRussia
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Berr A, Chabouté ME. The art of painting chromosome loops. Quant Plant Biol 2023; 4:e11. [PMID: 37901685 PMCID: PMC10600566 DOI: 10.1017/qpb.2023.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
How to get a metre of DNA into a tiny space while preserving its functional characteristics? This question seems easy to pose, but the answer is far from being trivial. Facing this riddle, salvation came from technical improvements in microscopy and in situ hybridisation techniques applied to cytogenetics. Here, we would like to look into the past at one of these pure cytogenetics articles that makes a breakthrough in addressing this question in plant science. Our choice fell on the work published two decades ago by Fransz et al. (2002). Besides the elegant manner in which DNA probes were organised to bring into light the out-looping arrangement of interphase chromosomes in Arabidopsis thaliana nuclei, this article perfectly illustrates that painting is not reserved to the fine art. As for whether emotional expression prioritised by artists can sometimes hide behind scientific empirical evidence, there is only a small step to make to the general case.
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Affiliation(s)
- Alexandre Berr
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. Front Plant Sci 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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Ru Y, Mandáková TM, Lysak MA, Koch MA. The evolutionary history of Cardamine bulbifera shows a successful rapid postglacial Eurasian range expansion in the absence of sexual reproduction. Ann Bot 2022; 130:245-263. [PMID: 35789248 PMCID: PMC9445599 DOI: 10.1093/aob/mcac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Sexual reproduction is known to drive plant diversification and adaptation. Here we investigate the evolutionary history and spatiotemporal origin of a dodecaploid (2n = 12x = 96) Eurasian deciduous woodland species, Cardamine bulbifera, which reproduces and spreads via vegetative bulb-like structures only. The species has been among the most successful range-expanding understorey woodland plants in Europe, which raises the question of the genetic architecture of its gene pool, since its hexaploid (2n = 6x = 48) but putatively outcrossing closest relative, C. quinquefolia, displays a smaller distribution range in Eastern Europe towards the Caucasus region. Cardamine bulbifera belongs to a small monophyletic clade of four species comprising also C. abchasica (2n = 2x = 16) and C. bipinnata (unknown ploidy) from the Caucasus region. METHODS We sequenced the genomes of the two polyploids and their two putative ancestors using Illumina short-read sequencing technology (×7-8 coverage). Covering the entire distribution range, genomic data were generated for 67 samples of the two polyploids (51 samples of C. bulbifera, 16 samples of C. quinquefolia) and 6 samples of the putative diploid taxa (4 samples of C. abchasica, 2 samples of C. bipinnata) to unravel the evolutionary origin of the polyploid taxa using phylogenetic reconstructions of biparentally and maternally inherited genetic sequence data. Ploidy levels of C. bulbifera and C. quinquefolia were analysed by comparative chromosome painting. We used genetic assignment analysis (STRUCTURE) and approximate Bayesian computation (ABC) modelling to test whether C. bulbifera represents genetically differentiated lineages and addressed the hypothesis of its hybrid origin. Comparative ecological modelling was applied to unravel possible niche differentiation among the two polyploid species. KEY RESULTS Cardamine bulbifera was shown to be a non-hybridogenous, auto-dodecaploid taxon of early Pleistocene origin, but with a history of past gene flow with its hexaploid sister species C. quinquefolia, likely during the last glacial maximum in shared refuge areas in Eastern Europe towards Western Turkey and the Crimean Peninsula region. The diploid Caucasian endemic C. abchasica is considered an ancestral species, which also provides evidence for the origin of the species complex in the Caucasus region. Cardamine bulbifera successfully expanded its distribution range postglacially towards Central and Western Europe accompanied by a transition to exclusively vegetative propagation. CONCLUSIONS A transition to vegetative propagation in C. bulbifera is hypothesized as the major innovation to rapidly expand its distribution range following postglacially progressing woodland vegetation throughout Europe. Preceding and introgressive gene flow from its sister species C. quinquefolia in the joint refuge area is documented. This transition and ecological differentiation may have been triggered by preceding introgressive gene flow from its sister species in the joint East European refuge areas.
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Affiliation(s)
- Yalu Ru
- Centre for Organismal Studies Heidelberg (COS), Department of Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Terezie M Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
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Yu F, Zhao X, Chai J, Ding X, Li X, Huang Y, Wang X, Wu J, Zhang M, Yang Q, Deng Z, Jiang J. Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. New Phytol 2022; 233:1953-1965. [PMID: 34874076 DOI: 10.1111/nph.17905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species. Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligo-based chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus. We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species. We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.
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Affiliation(s)
- Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Xinwang Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jin Chai
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueer Ding
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Xianhong Wang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Muqing Zhang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Qinghui Yang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
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Foria S, Magris G, Jurman I, Schwope R, De Candido M, De Luca E, Ivanišević D, Morgante M, Di Gaspero G. Extent of wild-to-crop interspecific introgression in grapevine (Vitis vinifera) as a consequence of resistance breeding and implications for the crop species definition. Hortic Res 2022; 9:uhab010. [PMID: 35039824 PMCID: PMC8801725 DOI: 10.1093/hr/uhab010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/18/2022] [Accepted: 09/25/2021] [Indexed: 05/31/2023]
Abstract
Over the past two centuries, introgression through repeated backcrossing has introduced disease resistance from wild grape species into the domesticated lineage Vitis vinifera subsp. sativa. Introgression lines are being cultivated over increasing vineyard surface areas, as their wines now rival in quality those obtained from preexisting varieties. There is, however, a lot of debate about whether and how wine laws defining commercial product categories, which are based on the classification of V. vinifera and interspecific hybrid grapes, should be revised to accommodate novel varieties that do not fit either category. Here, we developed a method of multilocus genotype analysis using short-read resequencing to identify haplotypic blocks of wild ancestry in introgression lines and quantify the physical length of chromosome segments free-of-introgression or with monoallelic and biallelic introgression. We used this genomic data to characterize species, hybrids and introgression lines and show that newly released resistant varieties contain 76.5-94.8% of V. vinifera DNA. We found that varietal wine ratings are not always commensurate with the percentage of V. vinifera ancestry and linkage drag of wild alleles around known resistance genes persists over at least 7.1-11.5 Mb, slowing down the recovery of the recurrent parental genome. This method also allowed us to identify the donor species of known resistance haplotypes, define the ancestry of wild genetic background in introgression lines with complex pedigrees, validate the ancestry of the historic varieties Concord and Norton, and unravel sample curation errors in public databases.
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Affiliation(s)
- Serena Foria
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
- Dr. Schär R&D Centre, Padriciano 99, 34149 Trieste, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Irena Jurman
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
| | - Rachel Schwope
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Massimo De Candido
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Elisa De Luca
- VCR Research Center, Vivai Cooperativi Rauscedo, Via Ruggero Forti 4, 33095 San Giorgio della Richinvelda, Italy
| | - Dragoslav Ivanišević
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21102 Novi Sad, Serbia
| | - Michele Morgante
- Istituto di Genomica Applicata,
via Jacopo Linussio, 51, 33100 Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via delle Scienze 206, 33100 Udine, Italy
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Meng Z, Wang Q, Khurshid H, Raza G, Han J, Wang B, Wang K. Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane. Front Plant Sci 2021; 12:731664. [PMID: 34512706 PMCID: PMC8429501 DOI: 10.3389/fpls.2021.731664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
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Romanenko SA, Malikov VG, Mahmoudi A, Golenishchev FN, Lemskaya NA, Pereira JC, Trifonov VA, Serdyukova NA, Ferguson-Smith MA, Aliabadian M, Graphodatsky AS. New Data on Comparative Cytogenetics of the Mouse-Like Hamsters ( Calomyscus Thomas, 1905) from Iran and Turkmenistan. Genes (Basel) 2021; 12:genes12070964. [PMID: 34202749 PMCID: PMC8304524 DOI: 10.3390/genes12070964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
The taxonomy of the genus Calomyscus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 Calomyscus individuals from different regions of Iran and Turkmenistan using a new set of chromosome painting probes from a Calomyscus sp. male (2n = 46, XY; Shahr-e-Kord-Soreshjan-Cheshme Maiak Province). We showed the retention of large syntenic blocks in karyotypes of individuals with identical chromosome numbers. The only rearrangement (fusion 2/21) differentiated Calomyscus elburzensis, Calomyscus mystax mystax, and Calomyscus sp. from Isfahan Province with 2n = 44 from karyotypes of C. bailwardi, Calomyscus sp. from Shahr-e-Kord, Chahar Mahal and Bakhtiari-Aloni, and Khuzestan-Izeh Provinces with 2n = 46. The individuals from Shahdad tunnel, Kerman Province with 2n = 51-52 demonstrated non-centric fissions of chromosomes 4, 5, and 6 of the 46-chromosomal form with the formation of separate small acrocentrics. A heteromorphic pair of chromosomes in a specimen with 2n = 51 resulted from a fusion of two autosomes. C-banding and chromomycin A3-DAPI staining after G-banding showed extensive heterochromatin variation between individuals.
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Affiliation(s)
- Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
- Correspondence: ; Tel.: +7-383-363-90-63
| | - Vladimir G. Malikov
- Zoological Institute (ZIN), Russian Academy of Sciences (RAS), 199034 Saint-Petersburg, Russia; (V.G.M.); (F.N.G.)
| | - Ahmad Mahmoudi
- Department of Biology, Faculty of Science, Urmia University, Urmia 5756151818, Iran;
| | - Feodor N. Golenishchev
- Zoological Institute (ZIN), Russian Academy of Sciences (RAS), 199034 Saint-Petersburg, Russia; (V.G.M.); (F.N.G.)
| | - Natalya A. Lemskaya
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
| | - Jorge C. Pereira
- Animal and Veterinary Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK;
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Natalia A. Serdyukova
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 OES, UK;
| | - Mansour Aliabadian
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Alexander S. Graphodatsky
- Institute of Molecular and Cellular Biology (IMCB), Siberian Branch of Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (N.A.L.); (V.A.T.); (N.A.S.); (A.S.G.)
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12
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Roco ÁS, Liehr T, Ruiz-García A, Guzmán K, Bullejos M. Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae). Genes (Basel) 2021; 12:617. [PMID: 33919402 PMCID: PMC8143290 DOI: 10.3390/genes12050617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.
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Affiliation(s)
- Álvaro S. Roco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany;
| | - Adrián Ruiz-García
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Kateryna Guzmán
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
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13
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Braz GT, Yu F, Zhao H, Deng Z, Birchler JA, Jiang J. Preferential meiotic chromosome pairing among homologous chromosomes with cryptic sequence variation in tetraploid maize. New Phytol 2021; 229:3294-3302. [PMID: 33222183 DOI: 10.1111/nph.17098] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Meiotic chromosome pairing between homoeologous chromosomes was reported in many nascent allopolyploids. Homoeologous pairing is gradually eliminated and replaced by exclusive homologous pairing in well-established allopolyploids, an evolutionary process referred to as the diploidization of allopolyploids. A fundamental question of the diploidization of allopolyploids is whether and to what extent the DNA sequence variation among homoeologous chromosomes contribute to the establishment of exclusive homologous chromosome pairing. We developed aneuploid tetraploid maize lines that contain three copies of chromosome 10 derived from inbred lines B73 and H99. We were able to identify the parental origin of each copy of chromosome 10 in the materials using oligonucleotide-based haplotype-specific chromosome painting. We demonstrate that the two identical copies of chromosome 10 from H99 pair preferentially over chromosome 10 from B73 in different stages of prophase I and metaphase I during meiosis. Thus, homologous chromosome pairing is favored to partners with the most similar DNA sequences and can be discriminated based on cryptic sequence variation. We propose that innate preference of homologous chromosome pairing exists in nascent allopolyploids and serves as the first layer that would eventually block all homoeologous chromosome pairing in allopolyploids.
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Affiliation(s)
- Guilherme T Braz
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Fan Yu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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14
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Furo IDO, Kretschmer R, O'Brien PCM, Pereira JCDC, Gunski RJ, Garnero ADV, O'Connor RE, Griffin DK, Ferguson-Smith MA, Oliveira EHCD. Cytotaxonomy of Gallinula melanops (Gruiformes, Rallidae): Karyotype evolution and phylogenetic inference. Genet Mol Biol 2021; 44:e20200241. [PMID: 33821875 PMCID: PMC8022357 DOI: 10.1590/1678-4685-gmb-2020-0241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/29/2021] [Indexed: 11/22/2022] Open
Abstract
Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus.
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Affiliation(s)
- Ivanete de Oliveira Furo
- Universidade Federal Rural da Amazônia (UFRA) Laboratório de Reprodução Animal (LABRAC), Parauapebas, PA, Brazil
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, RS, Brazil
- University of Kent, School of Biosciences, Canterbury, United Kingdom
| | - Patricia C M O'Brien
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Jorge Claudio da Costa Pereira
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
- University of Trás-os-Montes and Alto Douro (UTAD), Animal and Veterinary Research Centre (CECAV), Vila Real, Portugal
| | - Ricardo José Gunski
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas (PPGCB), São Gabriel, RS, Brazil
| | - Analía Del Valle Garnero
- Universidade Federal do Pampa, Programa de Pós-graduação em Ciências Biológicas (PPGCB), São Gabriel, RS, Brazil
| | | | | | - Malcolm A Ferguson-Smith
- University of Cambridge Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, Cambridge, United Kingdom
| | - Edivaldo Herculano Corrêa de Oliveira
- Instituto Evandro Chagas, Laboratório de Cultura de Tecidos e Citogenética (SAMAM), Ananindeua, PA, Brazil
- Universidade Federal do Pará, Instituto de Ciências Exatas e Naturais, Belém, PA, Brazil
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15
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Bi Y, Zhao Q, Yan W, Li M, Liu Y, Cheng C, Zhang L, Yu X, Li J, Qian C, Wu Y, Chen J, Lou Q. Flexible chromosome painting based on multiplex PCR of oligonucleotides and its application for comparative chromosome analyses in Cucumis. Plant J 2020; 102:178-186. [PMID: 31692131 DOI: 10.1111/tpj.14600] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 10/09/2019] [Accepted: 10/21/2019] [Indexed: 05/07/2023]
Abstract
Chromosome painting is a powerful technique for chromosome and genome studies. We developed a flexible chromosome painting technique based on multiplex PCR of a synthetic oligonucleotide (oligo) library in cucumber (Cucumis sativus L., 2n = 14). Each oligo in the library was associated with a universal as well as nested specific primers for amplification, which allow the generation of different probes from the same oligo library. We were also able to generate double-stranded labelled oligos, which produced much stronger signals than single-stranded labelled oligos, by amplification using fluorophore-conjugated primer pairs. Oligos covering cucumber chromosome 1 (Chr1) and chromosome 4 (Chr4) consisting of eight segments were synthesized in one library. Different oligo probes generated from the library painted the corresponding chromosomes/segments unambiguously, especially on pachytene chromosomes. This technique was then applied to study the homoeologous relationships among cucumber, C. hystrix and C. melo chromosomes based on cross-species chromosome painting using Chr4 probes. We demonstrated that the probe was feasible to detect interspecies chromosome homoeologous relationships and chromosomal rearrangement events. Based on its advantages and great convenience, we anticipate that this flexible oligo-painting technique has great potential for the studies of the structure, organization, and evolution of chromosomes in any species with a sequenced genome.
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Affiliation(s)
- Yunfei Bi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenkai Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengxue Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuxi Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chuntao Qian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Oliveira da Silva W, Malcher SM, Pereira AL, Pieczarka JC, Ferguson-Smith MA, O'Brien PCM, Mendes-Oliveira AC, Geise L, Nagamachi CY. Chromosomal Signatures Corroborate the Phylogenetic Relationships within Akodontini (Rodentia, Sigmodontinae). Int J Mol Sci 2020; 21:E2415. [PMID: 32244440 DOI: 10.3390/ijms21072415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/28/2020] [Accepted: 03/28/2020] [Indexed: 12/30/2022] Open
Abstract
Comparative chromosome-painting analysis among highly rearranged karyotypes of Sigmodontinae rodents (Rodentia, Cricetidae) detects conserved syntenic blocks, which are proposed as chromosomal signatures and can be used as phylogenetic markers. In the Akodontini tribe, the molecular topology (Cytb and/or IRBP) shows five low-supported clades (divisions: “Akodon”, “Bibimys”, “Blarinomys”, “Oxymycterus”, and “Scapteromys”) within two high-supported major clades (clade A: “Akodon”, “Bibimys”, and “Oxymycterus”; clade B: “Blarinomys” and “Scapteromys”). Here, we examine the chromosomal signatures of the Akodontini tribe by using Hylaeamysmegacephalus (HME) probes to study the karyotypes of Oxymycterus amazonicus (2n = 54, FN = 64) and Blarinomys breviceps (2n = 28, FN = 50), and compare these data with those from other taxa investigated using the same set of probes. We strategically employ the chromosomal signatures to elucidate phylogenetic relationships among the Akodontini. When we follow the evolution of chromosomal signature states, we find that the cytogenetic data corroborate the current molecular relationships in clade A nodes. We discuss the distinct events that caused karyotypic variability in the Oxymycterus and Blarinomys genera. In addition, we propose that Blarinomys may constitute a species complex, and that the taxonomy should be revised to better delimit the geographical boundaries and their taxonomic status.
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Romanenko SA, Smorkatcheva AV, Kovalskaya YM, Prokopov DY, Lemskaya NA, Gladkikh OL, Polikarpov IA, Serdyukova NA, Trifonov VA, Molodtseva AS, O'Brien PCM, Golenishchev FN, Ferguson-Smith MA, Graphodatsky AS. Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism. Genes (Basel) 2020; 11:E374. [PMID: 32235544 DOI: 10.3390/genes11040374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/23/2020] [Accepted: 03/27/2020] [Indexed: 11/21/2022] Open
Abstract
The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.
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Soares FAF, Carvalho CR, Sattler MC, Silva JC, Pinto DEE, Passamani PZ, Silva AJ, Clarindo WR. Plant Chromosome-Specific Probes by Microdissection of a Single Chromosome: Is That a Reality? Front Plant Sci 2020; 11:334. [PMID: 32273878 PMCID: PMC7113637 DOI: 10.3389/fpls.2020.00334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/06/2020] [Indexed: 05/26/2023]
Abstract
Painting plant chromosomes through chromosomal in situ suppression (CISS) hybridization has long been considered impracticable. Seeking to build specific and complex probes from a single microdissected chromosome, we employed human chromosomes as models to standardize all the necessary steps for application in plants. Human metaphases were used to define the adequate conditions for microdissection, chromosome DNA amplification and labeling through degenerate oligonucleotide-primed PCR, and in situ hybridization stringency. Subsequently, these methodologies were applied in the plant species Zea mays (chromosome 1) and Capsicum annuum (chromosome 7 or 8). The high quality of human and plant cytogenetic preparations and the meticulous standardization of each step, especially the most critical ones - microdissection and first round of DNA amplification - were crucial to eliminate the signs of non-specific hybridization and for direct application in plants. By overcoming these challenges, we obtained chromosome-specific probes, which allowed to achieve a clear and uniform painting of the entire target chromosomes with little or no background, evidencing their complexity and specificity. Despite the high amount of ubiquitous repetitive sequences in plant genomes, the main drawback for chromosome painting, we successfully employed our methodology on two plant species. Both have more than 80% repetitive sequences, which is compared to the human genome (66-69%). This is the first time that plant chromosome-specific probes were successfully obtained from a single A mitotic or meiotic microdissected chromosome. Thereby, we assume that chromosome painting through microdissection and CISS hybridization can now be considered a reality in the field of plant cytogenetics.
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Affiliation(s)
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, Brazil
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Bačovský V, Čegan R, Šimoníková D, Hřibová E, Hobza R. The Formation of Sex Chromosomes in Silene latifolia and S. dioica Was Accompanied by Multiple Chromosomal Rearrangements. Front Plant Sci 2020; 11:205. [PMID: 32180787 PMCID: PMC7059608 DOI: 10.3389/fpls.2020.00205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/11/2020] [Indexed: 05/02/2023]
Abstract
The genus Silene includes a plethora of dioecious and gynodioecious species. Two species, Silene latifolia (white campion) and Silene dioica (red campion), are dioecious plants, having heteromorphic sex chromosomes with an XX/XY sex determination system. The X and Y chromosomes differ mainly in size, DNA content and posttranslational histone modifications. Although it is generally assumed that the sex chromosomes evolved from a single pair of autosomes, it is difficult to distinguish the ancestral pair of chromosomes in related gynodioecious and hermaphroditic plants. We designed an oligo painting probe enriched for X-linked scaffolds from currently available genomic data and used this probe on metaphase chromosomes of S. latifolia (2n = 24, XY), S. dioica (2n = 24, XY), and two gynodioecious species, S. vulgaris (2n = 24) and S. maritima (2n = 24). The X chromosome-specific oligo probe produces a signal specifically on the X and Y chromosomes in S. latifolia and S. dioica, mainly in the subtelomeric regions. Surprisingly, in S. vulgaris and S. maritima, the probe hybridized to three pairs of autosomes labeling their p-arms. This distribution suggests that sex chromosome evolution was accompanied by extensive chromosomal rearrangements in studied dioecious plants.
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- *Correspondence: Václav Bačovský,
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Denisa Šimoníková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Roman Hobza,
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Xin H, Zhang T, Wu Y, Zhang W, Zhang P, Xi M, Jiang J. An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting. Plant J 2020; 101:253-264. [PMID: 31529535 DOI: 10.1111/tpj.14536] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/25/2019] [Accepted: 09/02/2019] [Indexed: 05/22/2023]
Abstract
The karyotype represents the basic genetic make-up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter-chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.
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Affiliation(s)
- Haoyang Xin
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yufeng Wu
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenli Zhang
- The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pingdong Zhang
- National Engineering Laboratory for Tree Breeding, College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Mengli Xi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
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21
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Liu Y, Wang X, Wei Y, Liu Z, Lu Q, Liu F, Zhang T, Peng R. Chromosome Painting Based on Bulked Oligonucleotides in Cotton. Front Plant Sci 2020; 11:802. [PMID: 32695125 PMCID: PMC7338755 DOI: 10.3389/fpls.2020.00802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/19/2020] [Indexed: 05/06/2023]
Abstract
Chromosome painting is one of the key technologies in cytogenetic research, which can accurately identify chromosomes or chromosome regions. Oligonucleotide (oligo) probes designed based on genome sequences have both flexibility and specificity, which would be ideal probes for fluorescence in situ hybridization (FISH) analysis of genome structure. In this study, the bulked oligos of the two arms of chromosome seven of cotton were developed based on the genome sequence of Gossypium raimondii (DD, 2n = 2× = 26), and each arm contains 12,544 oligos. Chromosome seven was easily identified in both D genome and AD genome cotton species using the bulked chromosome-specific painting probes. Together with 45S ribosomal DNA (rDNA) probe, the chromosome-specific painting probe was also successfully used to correct the chromosomal localization of 45S rDNA in G. raimondii. The study reveals that bulked oligos specific to a chromosome is a useful tool for chromosome painting in cotton.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, China
| | | | | | - Zhen Liu
- Anyang Institute of Technology, Anyang, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang,
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, China
- Renhai Peng,
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22
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Proskuryakova AA, Kulemzina AI, Perelman PL, Yudkin DV, Lemskaya NA, Okhlopkov IM, Kirillin EV, Farré M, Larkin DM, Roelke-Parker ME, O'Brien SJ, Bush M, Graphodatsky AS. Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species. Genes (Basel) 2019; 10:E857. [PMID: 31671864 DOI: 10.3390/genes10110857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 11/17/2022] Open
Abstract
: Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirk's Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB3.
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23
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Romanenko SA, Lyapunova EA, Saidov AS, O'Brien PCM, Serdyukova NA, Ferguson-Smith MA, Graphodatsky AS, Bakloushinskaya I. Chromosome Translocations as a Driver of Diversification in Mole Voles Ellobius (Rodentia, Mammalia). Int J Mol Sci 2019; 20:E4466. [PMID: 31510061 PMCID: PMC6769443 DOI: 10.3390/ijms20184466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/23/2022] Open
Abstract
The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous; consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Elena A Lyapunova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
| | - Abdusattor S Saidov
- Institute of Zoology and Parasitology, Academy of Sciences of Tajikistan, Dushanbe 734025, Tajikistan.
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
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24
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Zhang J, Parkinson J. PopNetD3-A Network-Based Web Resource for Exploring Population Structure. Genome Biol Evol 2019; 11:1730-1735. [PMID: 31095319 PMCID: PMC6668580 DOI: 10.1093/gbe/evz100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 11/14/2022] Open
Abstract
We present PopNetD3, a web tool that provides an integrated approach for the network-based visualization of population structure based on the PopNet clustering framework. Users first submit a tab-delimited file that defines diversity of SNPs across the genome which is subsequently processed by the PopNet backend to define patterns of conservation at the chromosome level. The resulting population structure is visualized through a dedicated D3-based tool, allowing users to interactively examine chromosomal regions predicted to share ancestry. We illustrate the capabilities of PopNetD3 through an analysis of 16 strains of Neisseria gonorrhoeae. PopNetD3 is capable of processing population data sets consisting of hundreds of individuals and is publicly available online at: http://compsysbio.org/popnetd3 Last Accessed: May 17, 2019.
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Affiliation(s)
- Javi Zhang
- Program in Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Ontario, Canada
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Ontario, Canada
- Corresponding author: E-mail:
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25
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Bakloushinskaya I, Lyapunova EA, Saidov AS, Romanenko SA, O’Brien PC, Serdyukova NA, Ferguson-Smith MA, Matveevsky S, Bogdanov AS. Rapid chromosomal evolution in enigmatic mammal with XX in both sexes, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 (Mammalia, Rodentia). Comp Cytogenet 2019; 13:147-177. [PMID: 31275526 PMCID: PMC6597615 DOI: 10.3897/compcytogen.v13i2.34224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/28/2019] [Indexed: 06/01/2023]
Abstract
Evolutionary history and taxonomic position for cryptic species may be clarified by using molecular and cytogenetic methods. The subterranean rodent, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 is one of three sibling species constituting the subgenus Ellobius Fischer, 1814, all of which lost the Y chromosome and obtained isomorphic XX sex chromosomes in both males and females. E.alaicus is evaluated by IUCN as a data deficient species because their distribution, biology, and genetics are almost unknown. We revealed specific karyotypic variability (2n = 52-48) in E.alaicus due to different Robertsonian translocations (Rbs). Two variants of hybrids (2n = 53, different Rbs) with E.tancrei Blasius, 1884 were found at the Northern slopes of the Alay Ridge and in the Naryn district, Kyrgyzstan. We described the sudden change in chromosome numbers from 2n = 50 to 48 and specific karyotype structure for mole voles, which inhabit the entrance to the Alay Valley (Tajikistan), and revealed their affiliation as E.alaicus by cytochrome b and fragments of nuclear XIST and Rspo1 genes sequencing. To date, it is possible to expand the range of E.alaicus from the Alay Valley (South Kyrgyzstan) up to the Ferghana Ridge and the Naryn Basin, Tien Shan at the north-east and to the Pamir-Alay Mountains (Tajikistan) at the west. The closeness of E.tancrei and E.alaicus is supported, whereas specific chromosome and molecular changes, as well as geographic distribution, verified the species status for E.alaicus. The case of Ellobius species accented an unevenness in rates of chromosome and nucleotide changes along with morphological similarity, which is emblematic for cryptic species.
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Affiliation(s)
- Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
| | - Elena A. Lyapunova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
| | - Abdusattor S. Saidov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, TajikistanPavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of TajikistanDushanbeTajikistan
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch RAS, Novosibirsk, RussiaInstitute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of SciencesNovosibirskRussia
- Novosibirsk State University, Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
| | - Patricia C.M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UKUniversity of CambridgeCambridgeUnited Kingdom
| | - Natalia A. Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch RAS, Novosibirsk, RussiaInstitute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of SciencesNovosibirskRussia
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UKUniversity of CambridgeCambridgeUnited Kingdom
| | - Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, RussiaVavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Alexey S. Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
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Kus A, Szymanowska-Pułka J, Kwasniewska J, Hasterok R. Detecting Brachypodium distachyon Chromosomes Bd4 and Bd5 in MH- and X-Ray-Induced Micronuclei Using mcFISH. Int J Mol Sci 2019; 20:ijms20112848. [PMID: 31212692 PMCID: PMC6612364 DOI: 10.3390/ijms20112848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/22/2019] [Accepted: 06/08/2019] [Indexed: 12/18/2022] Open
Abstract
Micronuclei are biomarkers of genotoxic effects and chromosomal instability. They are formed when chromosome fragments or whole chromosomes fail to disjoin into daughter nuclei. We present qualitative and quantitative analyses of the involvement of specific chromosome regions of chromosomes Bd4 and Bd5 in the formation of micronuclei of Brachypodium distachyon root tip cells following maleic hydrazide (MH) treatment and X-radiation. This is visualised by cytomolecular approaches using bacterial artificial chromosome (BAC)-based multicolour fluorescence in situ hybridisation (mcFISH) in combination with 5S and 25S rDNA probes. The results showed that the long arm of submetacentric chromosome Bd4 forms micronuclei at twice the frequency of its short arm, suggesting that the former is more prone to double-strand breaks (DSBs). In contrast, no difference was observed in the frequency of micronuclei derived from the long and short arms of submetacentric chromosome Bd5. Interestingly, the proximal region of the short arm of Bd5 is more prone to DSBs than its distal part. This demonstrates that 5S rDNA and 35S rDNA loci are not "hot spots" for DNA breaks after the application of these mutagens.
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Affiliation(s)
- Arita Kus
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Joanna Szymanowska-Pułka
- Department of Biophysics and Morphogenesis of Plants, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Jolanta Kwasniewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland.
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Skinner BM, Bacon J, Rathje CC, Larson EL, Kopania EEK, Good JM, Affara NA, Ellis PJI. Automated Nuclear Cartography Reveals Conserved Sperm Chromosome Territory Localization across 2 Million Years of Mouse Evolution. Genes (Basel) 2019; 10:genes10020109. [PMID: 30717218 PMCID: PMC6409866 DOI: 10.3390/genes10020109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Measurements of nuclear organization in asymmetric nuclei in 2D images have traditionally been manual. This is exemplified by attempts to measure chromosome position in sperm samples, typically by dividing the nucleus into zones, and manually scoring which zone a fluorescence in-situ hybridisation (FISH) signal lies in. This is time consuming, limiting the number of nuclei that can be analyzed, and prone to subjectivity. We have developed a new approach for automated mapping of FISH signals in asymmetric nuclei, integrated into an existing image analysis tool for nuclear morphology. Automatic landmark detection defines equivalent structural regions in each nucleus, then dynamic warping of the FISH images to a common shape allows us to generate a composite of the signal within the entire cell population. Using this approach, we mapped the positions of the sex chromosomes and two autosomes in three mouse lineages (Mus musculus domesticus, Mus musculus musculus and Mus spretus). We found that in all three, chromosomes 11 and 19 tend to interact with each other, but are shielded from interactions with the sex chromosomes. This organization is conserved across 2 million years of mouse evolution.
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Affiliation(s)
| | - Joanne Bacon
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
| | | | - Erica Lee Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA.
- Division of Biological Sciences, University of Montana, MT 59812, USA.
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28
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Albert PS, Zhang T, Semrau K, Rouillard JM, Kao YH, Wang CR, Danilova TV, Jiang J, Birchler JA. Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc Natl Acad Sci U S A 2019; 116:1679-85. [PMID: 30655344 DOI: 10.1073/pnas.1813957116] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Whole-chromosome painting probes were developed for each of the 10 chromosomes of maize by producing amplifiable libraries of unique sequences of oligonucleotides that can generate labeled probes through transcription reactions. These paints allow identification of individual homologous chromosomes for many applications as demonstrated in somatic root tip metaphase cells, in the pachytene stage of meiosis, and in interphase nuclei. Several chromosomal aberrations were examined as proof of concept for study of various rearrangements using probes that cover the entire chromosome and that label diverse varieties. The relationship of the supernumerary B chromosome and the normal chromosomes was examined with the finding that there is no detectable homology between any of the normal A chromosomes and the B chromosome. Combined with other chromosome-labeling techniques, a complete set of whole-chromosome oligonucleotide paints lays the foundation for future studies of the structure, organization, and evolution of genomes.
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de Oliveira Furo I, Kretschmer R, O'Brien PCM, Pereira JC, Del Valle Garnero A, Gunski RJ, Ferguson-Smith MA, de Oliveira EHC. Chromosome Painting in Neotropical Long- and Short-Tailed Parrots (Aves, Psittaciformes): Phylogeny and Proposal for a Putative Ancestral Karyotype for Tribe Arini. Genes (Basel) 2018; 9:E491. [PMID: 30309041 DOI: 10.3390/genes9100491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
Most Neotropical Psittacidae have a diploid number of 2n = 70, and a dichotomy in chromosome patterns. Long-tailed species have biarmed macrochromosomes, while short-tailed species have telo/acrocentric macrochromosomes. However, the use of chromosome painting has demonstrated that karyotype evolution in Psittacidae includes a high number of inter/intrachromosomal rearrangements. To determine the phylogeny of long- and short-tailed species, and to propose a putative ancestral karyotype for this group, we constructed homology maps of Pyrrhura frontalis (PFR) and Amazona aestiva (AAE), belonging to the long- and short-tailed groups, respectively. Chromosomes were analyzed by conventional staining and fluorescent in situ hybridization using whole chromosome paints of Gallusgallus and Leucopternis albicollis. Conventional staining showed a karyotype with 2n = 70 in both species, with biarmed macrochromosomes in PFR and telo/acrocentric chromosomes in AAE. Comparison of the results with the putative avian ancestral karyotype (PAK) showed fusions in PFR of PAK1p/PAK4q (PFR1) and PAK6/PAK7 (PFR6) with a paracentric inversion in PFR6. However, in AAE, there was only the fusion between PAK6/7 (AAE7) with a paracentric inversion. Our results indicate that PFR retained a more basal karyotype than long-tailed species previously studied, and AAE a more basal karyotype for Neotropical Psittacidae analyzed so far.
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Vcelar S, Jadhav V, Melcher M, Auer N, Hrdina A, Sagmeister R, Heffner K, Puklowski A, Betenbaugh M, Wenger T, Leisch F, Baumann M, Borth N. Karyotype variation of CHO host cell lines over time in culture characterized by chromosome counting and chromosome painting. Biotechnol Bioeng 2018; 115:165-173. [PMID: 28921524 DOI: 10.1002/bit.26453] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022]
Abstract
Genomic rearrangements are a common phenomenon in rapidly growing cell lines such as Chinese hamster ovary (CHO) cells, a feature that in the context of production of biologics may lead to cell line and product instability. Few methods exist to assess such genome wide instability. Here, we use the population distribution of chromosome numbers per cell as well as chromosome painting to quantify the karyotypic variation in several CHO host cell lines. CHO-S, CHO-K1 8 mM glutamine, and CHO-K1 cells adapted to grow in media containing no glutamine were analyzed over up to 6 months in culture. All three cell lines were clearly distinguishable by their chromosome number distribution and by the specific chromosome rearrangements that were present in each population. Chromosome Painting revealed a predominant karyotype for each cell line at the start of the experiment, completed by a large number of variants present in each population. Over time in culture, the predominant karyotype changed for CHO-S and CHO-K1, with the diversity increasing and new variants appearing, while CHO-K1 0 mM Gln preferred chromosome pattern increased in percent of the population over time. As control, Chinese hamster lung fibroblasts were shown to also contain an increasing number of variants over time in culture.
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Affiliation(s)
- Sabine Vcelar
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Norbert Auer
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Astrid Hrdina
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | | | | | - Anja Puklowski
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | | | - Till Wenger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria.,University of Natural Resources and Life Sciences, Vienna, Austria
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Zrzavá M, Hladová I, Dalíková M, Šíchová J, Õunap E, Kubíčková S, Marec F. Sex Chromosomes of the Iconic Moth Abraxas grossulariata (Lepidoptera, Geometridae) and Its Congener A. sylvata. Genes (Basel) 2018; 9:E279. [PMID: 29857494 DOI: 10.3390/genes9060279] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 01/28/2023] Open
Abstract
The magpie moth, Abraxas grossulariata, is an iconic species in which female heterogamety was discovered at the beginning of the 20th century. However, the sex chromosomes of this species have not yet been cytologically identified. We describe the sex chromosomes of A. grossulariata and its congener, A. sylvata. Although these species split only around 9.5 million years ago, and both species have the expected WZ/ZZ chromosomal system of sex determination and their sex chromosomes share the major ribosomal DNA (rDNA) representing the nucleolar organizer region (NOR), we found major differences between their karyotypes, including between their sex chromosomes. The species differ in chromosome number, which is 2n = 56 in A. grossularita and 2n = 58 in A. sylvata. In addition, A. grossularita autosomes exhibit massive autosomal blocks of heterochromatin, which is a very rare phenomenon in Lepidoptera, whereas the autosomes of A. sylvata are completely devoid of distinct heterochromatin. Their W chromosomes differ greatly. Although they are largely composed of female-specific DNA sequences, as shown by comparative genomic hybridization, cross-species W-chromosome painting revealed considerable sequence differences between them. The results suggest a relatively rapid molecular divergence of Abraxas W chromosomes by the independent spreading of female-specific repetitive sequences.
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Kretschmer R, de Lima VLC, de Souza MS, Costa AL, O’Brien PCM, Ferguson-Smith MA, de Oliveira EHC, Gunski RJ, Garnero ADV. Multidirectional chromosome painting in Synallaxis frontalis (Passeriformes, Furnariidae) reveals high chromosomal reorganization, involving fissions and inversions. Comp Cytogenet 2018; 12:97-110. [PMID: 29675139 PMCID: PMC5904361 DOI: 10.3897/compcytogen.v12i1.22344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
In this work we performed comparative chromosome painting using probes from Gallus gallus (GGA) Linnaeus, 1758 and Leucopternis albicollis (LAL) Latham, 1790 in Synallaxis frontalis Pelzeln, 1859 (Passeriformes, Furnariidae), an exclusively Neotropical species, in order to analyze whether the complex pattern of intrachromosomal rearrangements (paracentric and pericentric inversions) proposed for Oscines and Suboscines is shared with more basal species. S. frontalis has 82 chromosomes, similar to most Avian species, with a large number of microchromosomes and a few pairs of macrochromosomes. We found polymorphisms in pairs 1 and 3, where homologues were submetacentric and acrocentric. Hybridization of GGA probes showed syntenies in the majority of ancestral macrochromosomes, except for GGA1 and GGA2, which hybridized to more than one pair of chromosomes each. LAL probes confirmed the occurrence of intrachromosomal rearrangements in the chromosomes corresponding to GGA1q, as previously proposed for species from the order Passeriformes. In addition, LAL probes suggest that pericentric inversions or centromere repositioning were responsible for variations in the morphology of the heteromorphic pairs 1 and 3. Altogether, the analysis of our data on chromosome painting and the data published in other Passeriformes highlights chromosomal changes that have occurred during the evolution of Passeriformes.
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Affiliation(s)
- Rafael Kretschmer
- Programa de Pós-graduação em Genética e Biologia Molecular, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, RS, Brazil
| | - Vanusa Lilian Camargo de Lima
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Marcelo Santos de Souza
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Alice Lemos Costa
- Graduação em Ciências Biológicas, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Patricia C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Edivaldo Herculano Corrêa de Oliveira
- Faculdade de Ciências Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Ricardo José Gunski
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | - Analía Del Valle Garnero
- Programa de Pós-graduação em Ciências Biológicas, PPCGCB, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
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Machado MDA, Pieczarka JC, Silva FHR, O'Brien PCM, Ferguson-Smith MA, Nagamachi CY. Extensive Karyotype Reorganization in the Fish Gymnotus arapaima (Gymnotiformes, Gymnotidae) Highlighted by Zoo-FISH Analysis. Front Genet 2018; 9:8. [PMID: 29434621 PMCID: PMC5790778 DOI: 10.3389/fgene.2018.00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023] Open
Abstract
The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences. Recently whole chromosome painting (WCP) has been used for tracking the chromosomal evolution of the genus, showing highly reorganized karyotypes and the conserved synteny of the NOR bearing par within the clade G. carapo. In this study, painting probes derived from the chromosomes of G. carapo (GCA, 2n = 42, 30 m/sm + 12 st/a) were hybridized to the mitotic metaphases of G. arapaima (GAR, 2n = 44, 24 m/sm + 20 st/a). Our results uncovered chromosomal rearrangements and a high number of repetitive DNA regions. From the 12 chromosome pairs of G. carapo that can be individually differentiated (GCA1-3, 6, 7, 9, 14, 16, and 18-21), six pairs (GCA 1, 9, 14, 18, 20, 21) show conserved homology with GAR, five pairs (GCA 1, 9, 14, 20, 21) are also shared with cryptic species G. carapo 2n = 40 (34 m/sm + 6 st/a) and only the NOR bearing pair (GCA 20) is shared with G. capanema (GCP 2n = 34, 20 m/sm + 14 st/a). The remaining chromosomes are reorganized in the karyotype of GAR. Despite the close phylogenetic relationships of these species, our chromosome painting studies demonstrate an extensive reorganization of their karyotypes.
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Affiliation(s)
- Milla de Andrade Machado
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-Pará, Brazil
| | - Julio C Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-Pará, Brazil
| | - Fernando H R Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-Pará, Brazil
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Cleusa Y Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-Pará, Brazil
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Lamelas L, Arroyo M, Fernández FJ, Marchal JA, Sánchez A. Structural and Evolutionary Relationships in the Giant Sex Chromosomes of Three Microtus Species. Genes (Basel) 2018; 9:E27. [PMID: 29320452 PMCID: PMC5793180 DOI: 10.3390/genes9010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 01/03/2018] [Indexed: 11/18/2022] Open
Abstract
The genus Microtus has high karyotypic diversity. The existence of notable differences in the length of its sex chromosomes contributes to this variation. Variations in size are attributed to the enlargement of their heterochromatin content, which is of such magnitude in some species that they are referred to as "giant sex chromosomes". Here, we perform an intra- and interspecific analysis of the molecular composition of the heterochromatic blocks in three species with giant sex chromosomes (Microtus chrotorrhinus, M. cabrerae and M. agrestis). Our results show that the heterochromatic content is very similar in both the X and Y chromosomes of M. chrotorrhinus, and that their molecular composition is more closely related to the heterochromatic blocks of M. agrestis than to the sex heterochromatin of M. cabrerae; however, species-specific differences do clearly exist. Interestingly, the euchromatic regions of the X chromosome of all three of these species share a homologous region composed of heterochromatic-related sequences. Our results therefore reinforce the idea that certain similarities in the original organization of these X chromosomes could have facilitated their later enlargement.
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Affiliation(s)
- Luz Lamelas
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaén, Spain.
| | - María Arroyo
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaén, Spain.
| | - Francisco Javier Fernández
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaén, Spain.
| | - Juan Alberto Marchal
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaén, Spain.
| | - Antonio Sánchez
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaén, Spain.
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Braz GT, He L, Zhao H, Zhang T, Semrau K, Rouillard JM, Torres GA, Jiang J. Comparative Oligo-FISH Mapping: An Efficient and Powerful Methodology To Reveal Karyotypic and Chromosomal Evolution. Genetics 2018; 208:513-23. [PMID: 29242292 DOI: 10.1534/genetics.117.300344] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 12/05/2017] [Indexed: 11/18/2022] Open
Abstract
Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most nonmodel plant and animal species. We developed a novel chromosome identification system by selecting and labeling oligonucleotides (oligos) located in specific regions on every chromosome. We selected a set of 54,672 oligos (45 nt) based on single copy DNA sequences in the potato genome. These oligos generated 26 distinct FISH signals that can be used as a "bar code" or "banding pattern" to uniquely label each of the 12 chromosomes from both diploid and polyploid (4× and 6×) potato species. Remarkably, the same bar code can be used to identify the 12 homeologous chromosomes among distantly related Solanum species, including tomato and eggplant. Accurate karyotypes based on individually identified chromosomes were established in six Solanum species that have diverged for >15 MY. These six species have maintained a similar karyotype; however, modifications to the FISH signal bar code led to the discovery of two reciprocal chromosomal translocations in Solanum etuberosum and S. caripense We also validated these translocations by oligo-based chromosome painting. We demonstrate that the oligo-based FISH techniques are powerful new tools for chromosome identification and karyotyping research, especially for nonmodel plant species.
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Jetybayev IY, Bugrov AG, Buleu OG, Bogomolov AG, Rubtsov NB. Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization. Genes (Basel) 2017; 8:genes8110323. [PMID: 29137168 PMCID: PMC5704236 DOI: 10.3390/genes8110323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/16/2022] Open
Abstract
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family. The homologous regions of the neo-sex chromosomes were determined in closely related species with the painting procedure and image analysis with application of the Visualization of the Specific Signal in Silico software package. Results of these analyses and distribution of C-positive regions in the neo-sex chromosomes revealed details of the heteromorphization of the neo-sex chromosomes in species from both phylogenetic lineages of Pamphagidae grasshoppers. The hypothetical mechanism of the neo-Y degradation was suggested. It includes expansion of different repeats from the proximal neo-Y chromosome region by inversions, spreading them towards distal region. Amplification of these repeats leads to formation of C-positive regions and elimination of the C-negative regions located between them.
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Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Anton Gennadievich Bogomolov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
| | - Nikolay Borisovich Rubtsov
- The Federal Research Center, Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Lavrentjev Ave., 10, 630090 Novosibirsk, Russia.
- Novosibirsk State University, Department of Natural Sciences, Pirogov str., 2, 630090 Novosibirsk, Russia.
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Romanenko SA, Serdyukova NA, Perelman PL, Pavlova SV, Bulatova NS, Golenishchev FN, Stanyon R, Graphodatsky AS. Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting. Genes (Basel) 2017; 8:E215. [PMID: 28867774 PMCID: PMC5615349 DOI: 10.3390/genes8090215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 01/31/2023] Open
Abstract
It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information. Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics. We investigated the level of intrachromosomal rearrangement in the Arvicolinae subfamily, a species-rich taxon characterized by very high rate of karyotype evolution. We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes of four arvicolines (Microtus agrestis, Microtus arvalis, Myodes rutilus, and Dicrostonyx torquatus). These experiments allowed us to show the intrachromosomal rearrangements in the subfamily at a significantly higher level of resolution than previously described. We found a number of paracentric inversions in the karyotypes of M. agrestis and M. rutilus, as well as multiple inversions and a centromere shift in the karyotype of M. arvalis. We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Natalya A Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Svetlana V Pavlova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Nina S Bulatova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia.
| | | | - Roscoe Stanyon
- Department of Biology, Anthropology Laboratories, University of Florence, 50122 Florence, Italy.
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Synthetic Biological Unit, Novosibirsk State University, 630090 Novosibirsk, Russia.
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Abstract
With the advent of low cost, high-throughput genome sequencing technology, population genomic data sets are being generated for hundreds of species of pathogenic, industrial, and agricultural importance. The challenge is how best to analyze and visually display these complex data sets to yield intuitive representations capable of capturing complex evolutionary relationships. Here we present PopNet, a novel computational method that identifies regions of shared ancestry in the chromosomes of related strains through clustering patterns of genetic variation. These relationships are subsequently visualized within a network by a novel implementation of chromosome painting. We apply PopNet to three diverse populations that feature differential rates of recombination and demonstrate its ability to capture evolutionary relationships as well as associate traits to specific loci. Compared with existing tools, PopNet provides substantial advances by both removing the need to predefine a single reference genome that can bias interpretation of population structure, as well as its ability to visualize multiple evolutionary relationships, such as recombination events and shared ancestry, across hundreds of strains.
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Affiliation(s)
- Javi Zhang
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Asis Khan
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | - Andrea Kennard
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | - Michael E. Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, MD
| | - John Parkinson
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Program in Molecular Medicine, Hospital for Sick Children, Toronto, ON, Canada
- Departments of Computer Science and Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Du P, Zhuang L, Wang Y, Yuan L, Wang Q, Wang D, Dawadondup, Tan L, Shen J, Xu H, Zhao H, Chu C, Qi Z. Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes. Genome 2016; 60:93-103. [PMID: 27936984 DOI: 10.1139/gen-2016-0095] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. The oligo probes contained more nucleotides or more repeat units that produced stronger signals for more efficient chromosome painting. Four Th. bessarabicum-specific oligo probes were developed based on genomic DNA sequences of Th. bessarabicum chromosome arm 4JL, and one of them (oligo DP4J27982) was pooled with the oligo multiplex #1 to simultaneously detect wheat and Th. bessarabicum chromosomes for quick and accurate identification of Chinese Spring (CS) - Th. bessarabicum alien chromosome introgression lines. Oligo multiplex #4 revealed chromosome variations among CS and eight wheat cultivars by a single round of FISH analysis. This research demonstrated the high efficiency of using oligos and oligo multiplexes in chromosome identification and manipulation.
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Affiliation(s)
- Pei Du
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifang Zhuang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzhi Wang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Yuan
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Wang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Danrui Wang
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Dawadondup
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Lijun Tan
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Shen
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibin Xu
- b Faculty of Biology and Environmental Science, Nanjing Forestry University, Nanjing 210037, China
| | - Han Zhao
- c Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Chenggen Chu
- d Monsanto Company, 21120 Hwy 30, Filer, ID 83328, USA
| | - Zengjun Qi
- a State Key Laboratory of Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing Agricultural University, Nanjing 210095, China
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40
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Abstract
B chromosomes have so far been described in about 80 species of Coleoptera, mainly using conventional staining analysis. In this study, 152 individuals of the dung beetle Dichotomius sericeus (Coleoptera), collected from three isolated geographical areas in the State of Pernambuco, Brazil, were analyzed to determine the frequency, prevalence, distribution, meiotic behavior, and possible B chromosome origin. The cytogenetic analysis consisted of conventional staining, C-banding, triple fluorochrome staining (CMA3/DA/DAPI), and fluorescent in situ hybridization using ribosomal DNAs (rDNAs) and H3 histone gene as probes, as well as microdissection and chromosome painting of the B chromosome. The B chromosomes were detected in all populations analyzed. Analysis revealed the heterochromatic nature and the presence of G+C-rich blocks and 18S rDNA on the B chromosome. FISH with DNA from microdissected B chromosome painted the entire extension of the B chromosome for all populations, besides the pericentromeric regions of all the autosomes, as well as the X chromosome. Finally, cross-hybridization in nine related species of Dichotomius using the microdissected B chromosome as probe did not reveal any hybridization signal. The results suggest an intraspecific and monophyletic origin for B chromosomes in D. sericeus, probably from the second or third autosomal pair.
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Affiliation(s)
- Igor Costa Amorim
- a Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Brasil
| | - Diogo Milani
- b Instituto de Biociências, Departamento de Biologia, Universidade Estadual Paulista, Rio Claro, Brasil
| | | | - Marília França Rocha
- a Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Brasil
| | - Rita Cássia Moura
- a Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Brasil
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
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Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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Abstract
Chromosome painting (CP) refers to fluorescence in situ hybridization (FISH) of chromosome-specific DNA probes to identify large chromosome regions, chromosome arms, and whole chromosomes. For CP and CCP (comparative chromosome painting) in plants, most often, contigs of chromosome-specific bacterial artificial chromosomes (BAC) from the species of origin or a related species are used as painting probes. CP enables visualization and tracing of particular chromosome regions and/or chromosomes throughout all mitotic and meiotic stages as well as the corresponding interphase chromosome territories. CCP enables identification of large-scale homeologous chromosome regions and chromosomes shared among two or more species. Here, a step-by-step protocol for carrying out CP in Arabidopsis thaliana (Arabidopsis) and CCP in other crucifer taxa based on the use of Arabidopsis chromosome-specific BAC contigs is described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Czech Republic
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Abe Y, Miura T, Yoshida MA, Ujiie R, Kurosu Y, Kato N, Katafuchi A, Tsuyama N, Kawamura F, Ohba T, Inamasu T, Shishido F, Noji H, Ogawa K, Yokouchi H, Kanazawa K, Ishida T, Muto S, Ohsugi J, Suzuki H, Ishikawa T, Kamiya K, Sakai A. Analysis of chromosome translocation frequency after a single CT scan in adults. J Radiat Res 2016; 57:220-6. [PMID: 26874116 PMCID: PMC4915535 DOI: 10.1093/jrr/rrv090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/03/2015] [Indexed: 05/04/2023]
Abstract
We recently reported an increase in dicentric chromosome (DIC) formation after a single computed tomography (CT) scan (5.78-60.27 mSv: mean 24.24 mSv) and we recommended analysis of 2000 metaphase cells stained with Giemsa and centromere-FISH for dicentric chromosome assay (DCA) in cases of low-dose radiation exposure. In the present study, we analyzed the frequency of chromosome translocations using stored Carnoy's-fixed lymphocyte specimens from the previous study; these specimens were from 12 patients who were subject to chromosome painting of Chromosomes 1, 2 and 4. Chromosomes 1, 2 and 4 were analyzed in ∼5000 cells, which is equivalent to the whole-genome analysis of almost 2000 cells. The frequency of chromosome translocation was higher than the number of DICs formed, both before and after CT scanning. The frequency of chromosome translocations tended to be higher, but not significantly higher, in patients with a treatment history compared with patients without such a history. However, in contrast to the results for DIC formation, the frequency of translocations detected before and after the CT scan did not differ significantly. Therefore, analysis of chromosome translocation may not be a suitable assay for detecting chromosome aberrations in cases of low-dose radiation exposure from a CT scan. A significant increase in the frequency of chromosome translocations was not likely to be detected due to the high baseline before the CT scan; the high and variable frequency of translocations was probably due to multiple confounding factors in adults.
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Affiliation(s)
- Yu Abe
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tomisato Miura
- Department of Pathologic Analysis, Hirosaki University Graduate School of Health Sciences, Hirosaki, 036-8564, Japan
| | - Mitsuaki A Yoshida
- Department of Radiation Biology, Institute of Radiation Emergency Medicine, Hirosaki University, Hirosaki, 036-8564, Japan
| | - Risa Ujiie
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Yumiko Kurosu
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Nagisa Kato
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Atsushi Katafuchi
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Naohiro Tsuyama
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Fumihiko Kawamura
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Takashi Ohba
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tomoko Inamasu
- Department of Radiation Health Management, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Fumio Shishido
- Department of Radiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hideyoshi Noji
- Department of Cardiology and Hematology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kazuei Ogawa
- Department of Cardiology and Hematology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hiroshi Yokouchi
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kenya Kanazawa
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Takashi Ishida
- Department of Pulmonary Medicine, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Satoshi Muto
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Jun Ohsugi
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Hiroyuki Suzuki
- Department of Regenerative Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Tetsuo Ishikawa
- Department of Radiation Physics and Chemistry, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
| | - Kenji Kamiya
- Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Akira Sakai
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan Radiation Medical Science Center for the Fukushima Health Management Survey, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
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Loucas BD, Shuryak I, Cornforth MN. Three-Color Chromosome Painting as Seen through the Eyes of mFISH: Another Look at Radiation-Induced Exchanges and Their Conversion to Whole-Genome Equivalency. Front Oncol 2016; 6:52. [PMID: 27014627 PMCID: PMC4791380 DOI: 10.3389/fonc.2016.00052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/22/2016] [Indexed: 01/25/2023] Open
Abstract
Whole-chromosome painting (WCP) typically involves the fluorescent staining of a small number of chromosomes. Consequently, it is capable of detecting only a fraction of exchanges that occur among the full complement of chromosomes in a genome. Mathematical corrections are commonly applied to WCP data in order to extrapolate the frequency of exchanges occurring in the entire genome [whole-genome equivalency (WGE)]. However, the reliability of WCP to WGE extrapolations depends on underlying assumptions whose conditions are seldom met in actual experimental situations, in particular the presumed absence of complex exchanges. Using multi-fluor fluorescence in situ hybridization (mFISH), we analyzed the induction of simple exchanges produced by graded doses of 137Cs gamma rays (0–4 Gy), and also 1.1 GeV 56Fe ions (0–1.5 Gy). In order to represent cytogenetic damage as it would have appeared to the observer following standard three-color WCP, all mFISH information pertaining to exchanges that did not specifically involve chromosomes 1, 2, or 4 was ignored. This allowed us to reconstruct dose–responses for three-color apparently simple (AS) exchanges. Using extrapolation methods similar to those derived elsewhere, these were expressed in terms of WGE for comparison to mFISH data. Based on AS events, the extrapolated frequencies systematically overestimated those actually observed by mFISH. For gamma rays, these errors were practically independent of dose. When constrained to a relatively narrow range of doses, the WGE corrections applied to both 56Fe and gamma rays predicted genome-equivalent damage with a level of accuracy likely sufficient for most applications. However, the apparent accuracy associated with WCP to WGE corrections is both fortuitous and misleading. This is because (in normal practice) such corrections can only be applied to AS exchanges, which are known to include complex aberrations in the form of pseudosimple exchanges. When WCP to WGE corrections are applied to true simple exchanges, the results are less than satisfactory, leading to extrapolated values that underestimate the true WGE response by unacceptably large margins. Likely explanations for these results are discussed, as well as their implications for radiation protection. Thus, in seeming contradiction to notion that complex aberrations be avoided altogether in WGE corrections – and in violation of assumptions upon which these corrections are based – their inadvertent inclusion in three-color WCP data is actually required in order for them to yield even marginally acceptable results.
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Affiliation(s)
- Bradford D Loucas
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
| | - Igor Shuryak
- Center for Radiological Research, Columbia University , New York, NY , USA
| | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch , Galveston, TX , USA
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45
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Han Y, Zhang T, Thammapichai P, Weng Y, Jiang J. Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. Genetics 2015; 200:771-9. [PMID: 25971668 DOI: 10.1534/genetics.115.177642] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.
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46
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Abstract
To determine the appropriateness of chromosome painting for identifying genomic elements in rye, we microdissected the 1R and 1RS chromosomes from rye (Secale cereale L. var. King II) and wheat-rye addition line 1RS, respectively. Degenerate oligonucleotide primed - polymerase chain reaction (DOP-PCR) amplification of 1R and 1RS products from dissected chromosomes were used as probes to hybridize to metaphase chromosomes of rye, wheat-rye addition lines 1R and 1RS, translocation line 1RS.1BL, and allohexaploid triticale. The results showed that (i) the hybridization signal distribution patterns on rye chromosomes using 1R-derived DOP-PCR products as the probe were similar to those using 1RS-derived DOP-PCR products as the probe; (ii) 1R and (or) 1RS could not be distinguished from other rye chromosomes solely by the hybridization patterns using 1R- and (or) 1RS-derived DOP-PCR products as the probe; (iii) rye chromosomes and (or) rye chromosome fragments could be clearly identified in wheat-rye hybrids using either 1R- or 1RS-derived DOP-PCR products as the probe and could be more accurate in the nontelomeric region than using genomic in situ hybridization (GISH). Our results suggested that 1R- and (or) 1RS-derived DOP-PCR products contain many repetitive DNA sequences, are similar on different rye chromosomes, are R-genome specific, and can be used to identify rye chromosomes and chromosome fragments in wheat-rye hybrids. Our research widens the application range of chromosome painting in plants.
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Affiliation(s)
- Chuanliang Deng
- a Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China
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Lou Q, Zhang Y, He Y, Li J, Jia L, Cheng C, Guan W, Yang S, Chen J. Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis in Cucumis. Plant J 2014; 78:169-79. [PMID: 24635663 DOI: 10.1111/tpj.12453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/13/2014] [Accepted: 01/20/2014] [Indexed: 05/04/2023]
Abstract
Chromosome painting based on fluorescence in situ hybridization (FISH) has played an important role in chromosome identification and research into chromosome rearrangements, diagnosis of chromosome abnormalities and evolution in human and animal species. However, it has not been applied widely in plants due to the large amounts of dispersed repetitive sequences in chromosomes. In the present work, a chromosome painting method for single-copy gene pools in Cucumis sativus was successfully developed. Gene probes with sizes above 2 kb were detected consistently. A cucumber karyotype was constructed based on FISH using a cocktail containing chromosome-specific gene probes. This single-copy gene-based chromosome painting (ScgCP) technique was performed by PCR amplification, purification, pooling, labeling and hybridization onto chromosome spreads. Gene pools containing sequential genes with an interval less than 300 kb yielded painting patterns on pachytene chromosomes. Seven gene pools corresponding to individual chromosomes unambiguously painted each chromosome pair of C. sativus. Three mis-aligned regions on chromosome 4 were identified by the painting patterns. A probe pool comprising 133 genes covering the 8 Mb distal end of chromosome 4 was used to evaluate the potential utility of the ScgCP technique for chromosome rearrangement research through cross-species FISH in the Cucumis genus. Distinct painting patterns of this region were observed in C. sativus, C. melo and C. metuliferus species. A comparative chromosome map of this region was constructed between cucumber and melon. With increasing sequence resources, this ScgCP technique may be applied on any other sequenced species for chromosome painting research.
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Affiliation(s)
- Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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48
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Abstract
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here, we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a computationally efficient algorithm based on the recently developed “chromosome painting” algorithm, which characterizes patterns of haplotype sharing across a genome. We compare the average genome wide painting, which principally reflects clonal descent, with the painting for each site which additionally reflects the specific deviations at the site due to recombination. Using simulated data, we show that hot regions have consistently higher deviations from the genome wide average than normal regions. We applied our approach to previously analyzed Escherichia coli genomes and revealed that the new method is highly correlated with the number of recombination events affecting each site inferred by ClonalOrigin, a method that is only applicable to small numbers of genomes. Furthermore, we analyzed recombination hot regions in Campylobacter jejuni by using 200 genomes. We identified three recombination hot regions, which are enriched for genes related to membrane proteins. Our approach and its implementation, which is downloadable from https://github.com/bioprojects/orderedPainting, will help to develop a new phase of population genomic studies of recombination in prokaryotes.
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Affiliation(s)
- Koji Yahara
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, JapanInstitute of Medical Science, University of Tokyo, Tokyo, JapanInstitute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - M Azim Ansari
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Samuel K Sheppard
- Institute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom
| | - Daniel Falush
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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49
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McTavish EJ, Hillis DM. A Genomic Approach for Distinguishing between Recent and Ancient Admixture as Applied to Cattle. ACTA ACUST UNITED AC 2014; 105:445-456. [PMID: 24510946 PMCID: PMC4048551 DOI: 10.1093/jhered/esu001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 12/19/2013] [Indexed: 12/27/2022]
Abstract
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), which uses the nonrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient types of admixture, and applied it to the reconstruction of admixture in cattle. Cattle are descendants of 2 independently domesticated lineages, taurine and indicine, which diverged more than 200 000 years ago. Several breeds have hybrid ancestry between these divergent lineages. Using 47 506 single-nucleotide polymorphisms, we analyzed the genomic architecture of the ancestry of 1369 individuals. We focused on 4 groups with admixed ancestry, including 2 anciently admixed African breeds (n = 58; n = 43), New World cattle of Spanish origin (n = 51), and known recent hybrids (n = 46). We estimated the ancestry of chromosomal regions for each individual and used the SBS metric to differentiate the timing of admixture among groups and among individuals within groups. By comparing SBS values of test individuals with standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed cattle. We also estimated ancestry at the chromosomal scale. The X chromosome exhibits reduced indicine ancestry in recent hybrid, New World, and western African cattle, with virtually no evidence of indicine ancestry in New World cattle.
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Affiliation(s)
- Emily Jane McTavish
- From the Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 (McTavish and Hillis); and the Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 (McTavish).
| | - David M Hillis
- From the Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 (McTavish and Hillis); and the Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045 (McTavish)
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50
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Mandáková T, Marhold K, Lysak MA. The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. New Phytol 2014; 201:982-992. [PMID: 24400905 DOI: 10.1111/nph.12567] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 09/23/2013] [Indexed: 05/18/2023]
Abstract
The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5) yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
| | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
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