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Silva GS, Souza MM, Pamponét VDCC, Micheli F, de Melo CAF, de Oliveira SG, Costa EA. Cytogenomic Characterization of Transposable Elements and Satellite DNA in Passiflora L. Species. Genes (Basel) 2024; 15:418. [PMID: 38674353 PMCID: PMC11049143 DOI: 10.3390/genes15040418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The species Passiflora alata, P. cincinnata, and P. edulis have great economic value due to the use of their fruits for human consumption. In this study, we compared the repetitive genome fractions of these three species. The compositions of the repetitive DNA of these three species' genomes were analyzed using clustering and identification of the repetitive sequences with RepeatExplorer. It was found that repetitive DNA content represents 74.70%, 66.86%, and 62.24% of the genome of P. alata, P. edulis, and P. cincinnata, respectively. LTR Ty3/Gypsy retrotransposons represent the highest genome proportions in P. alata and P. edulis, while Ty1/Copia comprises the largest proportion of P. cincinnata genome. Chromosomal mapping by Fluorescent In Situ Hybridization (FISH) showed that LTR retrotransposons have a dispersed distribution along chromosomes. The subtelomeric region of chromosomes is where 145 bp satellite DNA is located, suggesting that these elements may play important roles in genome structure and organization in these species. In this work, we obtained the first global characterization of the composition of repetitive DNA in Passiflora, showing that an increase in genome size is related to an increase in repetitive DNA, which represents an important evolutionary route for these species.
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Affiliation(s)
- Gonçalo Santos Silva
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Margarete Magalhães Souza
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Vanessa de Carvalho Cayres Pamponét
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Fabienne Micheli
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Cláusio Antônio Ferreira de Melo
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
| | - Sárah Gomes de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 01049-010, SP, Brazil;
| | - Eduardo Almeida Costa
- Laboratório de Melhoramento de Plantas, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil; (G.S.S.); (V.d.C.C.P.); (F.M.); (C.A.F.d.M.); (E.A.C.)
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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] [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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Maravilla AJ, Rosato M, Rosselló JA. Interstitial Telomeric-like Repeats (ITR) in Seed Plants as Assessed by Molecular Cytogenetic Techniques: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:2541. [PMID: 34834904 PMCID: PMC8621592 DOI: 10.3390/plants10112541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 05/12/2023]
Abstract
The discovery of telomeric repeats in interstitial regions of plant chromosomes (ITRs) through molecular cytogenetic techniques was achieved several decades ago. However, the information is scattered and has not been critically evaluated from an evolutionary perspective. Based on the analysis of currently available data, it is shown that ITRs are widespread in major evolutionary lineages sampled. However, their presence has been detected in only 45.6% of the analysed families, 26.7% of the sampled genera, and in 23.8% of the studied species. The number of ITR sites greatly varies among congeneric species and higher taxonomic units, and range from one to 72 signals. ITR signals mostly occurs as homozygous loci in most species, however, odd numbers of ITR sites reflecting a hemizygous state have been reported in both gymnosperm and angiosperm groups. Overall, the presence of ITRs appears to be poor predictors of phylogenetic and taxonomic relatedness at most hierarchical levels. The presence of ITRs and the number of sites are not significantly associated to the number of chromosomes. The longitudinal distribution of ITR sites along the chromosome arms indicates that more than half of the ITR presences are between proximal and terminal locations (49.5%), followed by proximal (29.0%) and centromeric (21.5%) arm regions. Intraspecific variation concerning ITR site number, chromosomal locations, and the differential presence on homologous chromosome pairs has been reported in unrelated groups, even at the population level. This hypervariability and dynamism may have likely been overlooked in many lineages due to the very low sample sizes often used in cytogenetic studies.
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Affiliation(s)
| | | | - Josep A. Rosselló
- Jardín Botánico, ICBiBE, Universitat de València, c/Quart 80, E-46008 València, Spain; (A.J.M.); (M.R.)
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Pamponét VCC, Souza MM, Silva GS, Micheli F, de Melo CAF, de Oliveira SG, Costa EA, Corrêa RX. Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA. BMC Genomics 2019; 20:262. [PMID: 30940088 PMCID: PMC6444444 DOI: 10.1186/s12864-019-5576-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. RESULTS Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed. CONCLUSION P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.
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MESH Headings
- Chromosome Mapping
- Chromosomes, Plant
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Satellite/classification
- DNA, Satellite/genetics
- High-Throughput Nucleotide Sequencing
- In Situ Hybridization, Fluorescence
- Passiflora/genetics
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5S/genetics
- Retroelements/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Vanessa Carvalho Cayres Pamponét
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Margarete Magalhães Souza
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Gonçalo Santos Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Cláusio Antônio Ferreira de Melo
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Sarah Gomes de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão, 14 – Butantã, São Paulo, SP CEP 05508-090 Brazil
| | - Eduardo Almeida Costa
- Núcleo de Biologia Computacional e Gestão de Informações Biotecnológicas (NBCGIB), Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
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Mlinarec J, Skuhala A, Jurković A, Malenica N, McCann J, Weiss-Schneeweiss H, Bohanec B, Besendorfer V. The Repetitive DNA Composition in the Natural Pesticide Producer Tanacetum cinerariifolium: Interindividual Variation of Subtelomeric Tandem Repeats. FRONTIERS IN PLANT SCIENCE 2019; 10:613. [PMID: 31156676 PMCID: PMC6532368 DOI: 10.3389/fpls.2019.00613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/25/2019] [Indexed: 05/02/2023]
Abstract
Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.), a plant species endemic to the east Adriatic coast, is used worldwide for production of the organic insecticide, pyrethrin. Most studies concerning Dalmatian pyrethrum have focused on its morphological and biochemical traits relevant for breeding. However, little is known about the chromosomal evolution and genome organization of this species. Our study aims are to identify, classify, and characterize repetitive DNA in the T. cinerariifolium genome using clustering analysis of a low coverage genomic dataset. Repetitive DNA represents about 71.63% of the genome. T. cinerariifolium exhibits linked 5S and 35S rDNA configuration (L-type). FISH reveals amplification of interstitial telomeric repeats (ITRs) in T. cinerariifolium. Of the three newly identified satellite DNA families, TcSAT1 and TcSAT2 are located subterminally on most of T. cinerariifolium chromosomes, while TcSAT3 family is located intercalary within the longer arm of two chromosome pairs. FISH reveals high levels of polymorphism of the TcSAT1 and TcSAT2 sites by comparative screening of 28 individuals. TcSAT2 is more variable than TcSAT1 regarding the number and position of FISH signals. Altogether, our data highlights the dynamic nature of DNA sequences associated with subtelomeres in T. cinerariifolium and suggests that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Jelena Mlinarec
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | - Ana Skuhala
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Adela Jurković
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Nenad Malenica
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
| | - Jamie McCann
- Institute of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- *Correspondence: Jelena Mlinarec, orcid.org/0000-0002-2627-5374 Hanna Weiss-Schneeweiss, orcid.org/0000-0002-9530-6808
| | | | - Višnja Besendorfer
- Division of Molecular Biology, Department of Biology, Faculty of Science, Zagreb, Croatia
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Chen NWG, Thareau V, Ribeiro T, Magdelenat G, Ashfield T, Innes RW, Pedrosa-Harand A, Geffroy V. Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:1185. [PMID: 30154814 PMCID: PMC6102362 DOI: 10.3389/fpls.2018.01185] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/24/2018] [Indexed: 05/10/2023]
Abstract
Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (Phaseolus vulgaris), the Co-2 anthracnose resistance (R) locus corresponds to a cluster of nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant R genes. To study the recent evolution of this R gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago. Co-2 is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within khipu satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the Co-2 cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the Co-2 cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of R genes. We propose that chromosome ends could act as R gene incubators in many plant genomes.
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Affiliation(s)
- Nicolas W. G. Chen
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics, Federal University of Pernambuco, Recife, Brazil
| | - Ghislaine Magdelenat
- Genoscope/Commissariat à l’Energie Atomique-Centre National de Séquençage, Evry, France
| | - Tom Ashfield
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, IN, United States
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- *Correspondence: Valérie Geffroy,
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Li G, Wang H, Lang T, Li J, La S, Yang E, Yang Z. New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents. PLANTA 2016; 244:865-76. [PMID: 27290728 DOI: 10.1007/s00425-016-2554-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/06/2016] [Indexed: 05/19/2023]
Abstract
New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.
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Affiliation(s)
- Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Hongjin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Tao Lang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Jianbo Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Shixiao La
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.
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Koo DH, Zhao H, Jiang J. Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH. Chromosome Res 2016; 24:467-480. [PMID: 27590598 DOI: 10.1007/s10577-016-9537-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 02/05/2023]
Abstract
Tandemly repetitive DNA sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize (Zea mays), including the 180-bp knob repeat, the telomeric (TTTAGGG)n repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat. Although few transcripts derived from these four repeats were found in the expressed sequence tag and RNA-seq databases, RNA-FISH consistently detected the transcripts from three of the four repeats on interphase nuclei, suggesting that the transcripts from the three repeats are largely integrated into chromatin. The transcripts from the knob and telomeric repeats were mapped to the related DNA loci. In contrast, the transcripts from the CentC repeats were mainly localized to the nucleolus, although nucleoplasmic CentC transcripts were also detectable. The nucleolus and nuclear RNAs appeared to be important for the nuclear localization for at least one centromeric protein, Mis12. We demonstrate that RNA-FISH is a powerful tool to assess the level of transcription as well as to physically map the nuclear locations of the transcripts derived from satellite repeats.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Abstract
Fluorescence in situ hybridization (FISH) has become one of the most important technologies applied in plant molecular cytogenetic research. FISH technique has been not only well applied in physical mapping and genomic studies, but also served as an indispensable tool in tracing the individual chromosome during cell division. This chapter provides protocols for basic FISH analysis using rice as a model, which can also be adapted to other model plant species.
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Affiliation(s)
- Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, No 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, No 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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Heitkam T, Petrasch S, Zakrzewski F, Kögler A, Wenke T, Wanke S, Schmidt T. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica. Chromosome Res 2015; 23:791-806. [DOI: 10.1007/s10577-015-9500-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/30/2022]
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11
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Mehrotra S, Goyal V. Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function. GENOMICS, PROTEOMICS & BIOINFORMATICS 2014; 12:164-71. [PMID: 25132181 PMCID: PMC4411372 DOI: 10.1016/j.gpb.2014.07.003] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 06/29/2014] [Accepted: 07/03/2014] [Indexed: 12/27/2022]
Abstract
Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150-400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as "tuning knobs" in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences.
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Affiliation(s)
- Shweta Mehrotra
- Department of Botany, University of Delhi, Delhi 110007, India.
| | - Vinod Goyal
- Department of Botany, University of Delhi, Delhi 110007, India
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Richard MMS, Chen NWG, Thareau V, Pflieger S, Blanchet S, Pedrosa-Harand A, Iwata A, Chavarro C, Jackson SA, Geffroy V. The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833. FRONTIERS IN PLANT SCIENCE 2013; 4:109. [PMID: 24137164 PMCID: PMC3797529 DOI: 10.3389/fpls.2013.00109] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/09/2013] [Indexed: 05/10/2023]
Abstract
Subtelomeric regions in eukaryotic organisms are known for harboring species-specific tandemly repeated satellite sequences. However, studies on the molecular organization and evolution of subtelomeric repeats are scarce, especially in plants. Khipu is a satellite DNA of 528-bp repeat unit, specific of the Phaseolus genus, with a subtelomeric distribution in common bean, P. vulgaris. To investigate the genomic organization and the evolution of khipu, we performed genome-wide analysis on the complete genome sequence of the common bean genotype G19833. We identified 2,460 khipu units located at most distal ends of the sequenced regions. Khipu units are arranged in discrete blocks of 2-55 copies and are heterogeneously distributed among the different chromosome ends of G19833 (from 0 to 555 khipus units per chromosome arm). Phylogenetically related khipu units are spread between numerous chromosome ends, suggesting frequent exchanges between non-homologous subtelomeres. However, most subclades contain numerous khipu units from only one or few chromosome ends indicating that local duplication is also driving khipu expansion. Unexpectedly, we also identified 81 khipu units located at centromeres. All the centromeric khipu units belong to a single divergent clade also comprised of a few units from several subtelomeres, suggesting that a few sequence exchanges between centromeres and subtelomeres took place in the common bean genome. The divergence and low copy number of these centromeric units from the subtelomeric units could explain why they were not detected by FISH (Fluorescence in situ Hybridization) although it can not be excluded that these centromeric units may have resulted from errors in the pseudomolecule assembly. Altogether our data highlight extensive sequence exchanges in subtelomeres between non-homologous chromosomes in common bean and confirm that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Manon M. S. Richard
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Nicolas W. G. Chen
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Vincent Thareau
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Stéphanie Pflieger
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
- Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Sophie Blanchet
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Universidade Federal de Pernambuco, Rua Nelson Chaves s/nRecife, Pernambuco, Brazil
| | - Aiko Iwata
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Valérie Geffroy
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche AgronomiqueGif-sur-Yvette, France
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13
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Abstract
Development of techniques to analyze pachytene chromosomes has greatly overcome most of the difficulties in cytological studies of rice chromosomes caused by their small size. Visualization of meiotic chromosomes has now become routine in cytogenetic studies in this species. This chapter provides protocols on basic meiotic chromosome preparation, FISH analysis, and immunocytology in rice.
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Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses. Methods Mol Biol 2012; 956:13-27. [PMID: 23135841 DOI: 10.1007/978-1-62703-194-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful method to visualize DNA sequences in the context of the whole chromosome. Yet despite the value of FISH analysis for cytogenetic studies, there are surprisingly few labs that are able to adapt the technique for their experiments in chromosomal and genome biology. Here we present a comprehensive FISH protocol acquired from over 20 years of collective experience using different plant species. Our description uses rice as a model for performing a complete FISH procedure, but the protocol can be readily adapted for other plant species. We have provided more specialized instruction beyond routine FISH, which includes the preparation of meiotic and mitotic samples suitable for FISH analysis, procedures for direct and indirect labeling of DNA probes, and techniques for increasing signal strength using layers of antibodies.
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15
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Rosato M, Galián JA, Rosselló JA. Amplification, contraction and genomic spread of a satellite DNA family (E180) in Medicago (Fabaceae) and allied genera. ANNALS OF BOTANY 2012; 109:773-82. [PMID: 22186276 PMCID: PMC3286279 DOI: 10.1093/aob/mcr309] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Satellite DNA is a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNA is an important element in genome organization and evolution in plants. Here we assess the presence and physical distribution of the repetitive DNA E180 family in Medicago and allied genera. Our goals were to gain insight into the karyotype evolution of Medicago using satellite DNA markers, and to evaluate the taxonomic and phylogenetic signal of a satellite DNA family in a genus hypothesized to have a complex evolutionary history. METHODS Seventy accessions from Medicago, Trigonella, Melilotus and Trifolium were analysed by PCR to assess the presence of the repetitive E180 family, and fluorescence in situ hybridization (FISH) was used for physical mapping in somatic chromosomes. KEY RESULTS The E180 repeat unit was PCR-amplified in 37 of 40 taxa in Medicago, eight of 12 species of Trigonella, six of seven species of Melilotus and in two of 11 Trifolium species. Examination of the mitotic chromosomes revealed that only 13 Medicago and two Trigonella species showed FISH signals using the E180 probe. Stronger hybridization signals were observed in subtelomeric and interstitial loci than in the pericentromeric loci, suggesting this satellite family has a preferential genomic location. Not all 13 Medicago species that showed FISH localization of the E180 repeat were phylogenetically related. However, nine of these species belong to the phylogenetically derived clade including the M. sativa and M. arborea complexes. CONCLUSIONS The use of the E180 family as a phylogenetic marker in Medicago should be viewed with caution. Its amplification appears to have been produced through recurrent and independent evolutionary episodes in both annual and perennial Medicago species as well as in basal and derived clades.
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Affiliation(s)
- Marcela Rosato
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
| | - José A. Galián
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
| | - Josep A. Rosselló
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
- Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300 Blanes, Catalonia, Spain
- For correspondence. E-mail
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16
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Organization and evolution of subtelomeric satellite repeats in the potato genome. G3-GENES GENOMES GENETICS 2011; 1:85-92. [PMID: 22384321 PMCID: PMC3276127 DOI: 10.1534/g3.111.000125] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 05/03/2011] [Indexed: 12/30/2022]
Abstract
Subtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. A common feature associated with subtelomeric regions in different eukaryotes is the presence of long arrays of tandemly repeated satellite sequences. However, studies on molecular organization and evolution of subtelomeric repeats are rare. We isolated two subtelomeric repeats, CL14 and CL34, from potato (Solanum tuberosum). The CL14 and CL34 repeats are organized as independent long arrays, up to 1-3 Mb, of 182 bp and 339 bp monomers, respectively. The CL14 and CL34 repeat arrays are directly connected with the telomeric repeats at some chromosomal ends. The CL14 repeat was detected at the subtelomeric regions among highly diverged Solanum species, including tomato (Solanum lycopersicum). In contrast, CL34 was only found in potato and its closely related species. Interestingly, the CL34 repeat array was always proximal to the telomeres when both CL14 and CL34 were found at the same chromosomal end. In addition, the CL34 repeat family showed more sequence variability among monomers compared with the CL14 repeat family. We conclude that the CL34 repeat family emerged recently from the subtelomeric regions of potato chromosomes and is rapidly evolving. These results provide further evidence that subtelomeric domains are among the most dynamic regions in eukaryotic genomes.
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17
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Koo DH, Han F, Birchler JA, Jiang J. Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome. Genome Res 2011; 21:908-14. [PMID: 21518739 DOI: 10.1101/gr.116202.110] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Centromeres are determined by poorly understood epigenetic mechanisms. Centromeres can be activated or inactivated without changing the underlying DNA sequences. However, virtually nothing is known about the epigenetic transition of a centromere from an active to an inactive state because of the lack of examples of the same centromere exhibiting alternative forms and being distinguishable from other centromeres. The centromere of the supernumerary B chromosome of maize provides such an opportunity because its functional core can be cytologically tracked, and an inactive version of the centromere is available. We developed a DNA fiber-based technique that can be used to assess the levels of cytosine methylation associated with repetitive DNA sequences. We report that DNA sequences in the normal B centromere exhibit hypomethylation. This methylation pattern is not affected by the genetic background or structural rearrangement of the B chromosome, but is slightly changed when the B chromosome is transferred to oat as an addition chromosome. In contrast, an inactive version of this same centromere exhibits hypermethylation, indicating that the inactive centromere was modified into a different epigenetic state at the DNA level.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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18
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Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping. Methods Mol Biol 2010. [PMID: 21181534 DOI: 10.1007/978-1-61737-957-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We developed a simple technique to mechanically stretch maize pachytene chromosomes more than 20 times longer than their original size. A modified Carnoy's II solution (6:3:1) ethanol:acetic acid:chloroform was used to fix the meiotic sample. The super-stretched pachytene chromosomes produced from this procedure can be directly used in conventional fluorescence in situ hybridization (FISH) experiments and also for the immunofluorescent in situ detection of DNA methylation. This technique adds a new dimension and higher resolving power to pachytene chromosome-based molecular cytogenetics research.
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19
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Non-homologous chromosome pairing and crossover formation in haploid rice meiosis. Chromosoma 2010; 120:47-60. [DOI: 10.1007/s00412-010-0288-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 07/15/2010] [Accepted: 07/19/2010] [Indexed: 12/17/2022]
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20
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Yin BL, Guo L, Zhang DF, Terzaghi W, Wang XF, Liu TT, He H, Cheng ZK, Deng XW. Integration of cytological features with molecular and epigenetic properties of rice chromosome 4. MOLECULAR PLANT 2008; 1:816-829. [PMID: 19825584 DOI: 10.1093/mp/ssn037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-level transcriptional activity. To better understand this chromosomal organization, we created a model based on the statistical distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining. Fluorescence in-situ hybridization (FISH) experiments using a set of bacterial artificial chromosome (BAC) clones from chromosome 4 placed all 18 clones in the region predicted by the model. Elevated levels of H3K4 di- and tri-methylation detected by chromatin-immunoprecipitation (ChIP) on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions. Small RNAs were more abundant in the heterochromatic regions. To validate these findings, H3K4 trimethylation, H3K9 acetylation, H4K12 acetylation, and H3K9 di- and tri-methylation of 19 individual genes were measured by ChIP-PCR. Genes in heterochromatic regions had elevated H3K9 di- and tri-methylation while genes in euchromatic regions had elevated levels of the other three modifications. We also assayed cytosine methylation of these genes using the restriction enzymes McrBC, HapII, and Msp I. This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated. These results suggest that local transcriptional activity may reflect the organization of the corresponding part of the chromosome. They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptional activity.
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Affiliation(s)
- Ben-Liang Yin
- National Institute of Biological Sciences, Beijing 102206, China
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21
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Zhang W, Wang X, Yu Q, Ming R, Jiang J. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res 2008; 18:1938-43. [PMID: 18593814 DOI: 10.1101/gr.078808.108] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sex chromosomes evolved from autosomes. Recombination suppression in the sex-determining region and accumulation of deleterious mutations lead to degeneration of the Y chromosomes in many species with heteromorphic X/Y chromosomes. However, how the recombination suppressed domain expands from the sex-determining locus to the entire Y chromosome remains elusive. The Y chromosome of papaya (Carica papaya) diverged from the X chromosome approximately 2-3 million years ago and represents one of the most recently emerged Y chromosomes. Here, we report that the male-specific region of the Y chromosome (MSY) spans approximately 13% of the papaya Y chromosome. Interestingly, the centromere of the Y chromosome is embedded in the MSY. The centromeric domain within the MSY has accumulated significantly more DNA than the corresponding X chromosomal domain, which leads to abnormal chromosome pairing. We observed four knob-like heterochromatin structures specific to the MSY. Fluorescence in situ hybridization and immunofluorescence assay revealed that the DNA sequences associated with the heterochromatic knobs are highly divergent and heavily methylated compared with the sequences in the corresponding X chromosomal domains. These results suggest that DNA methylation and heterochromatinization play an important role in the early stage of sex chromosome evolution.
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Affiliation(s)
- Wenli Zhang
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
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22
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Abstract
Several lines of evidence suggest that, within a lineage, particular genomic regions are subject to instability that can lead to specific types of chromosome rearrangements important in species incompatibility. Within family Macropodidae (kangaroos, wallabies, bettongs, and potoroos), which exhibit recent and extensive karyotypic evolution, rearrangements involve chiefly the centromere. We propose that centromeres are the primary target for destabilization in cases of genomic instability, such as interspecific hybridization, and participate in the formation of novel chromosome rearrangements. Here we use standard cytological staining, cross-species chromosome painting, DNA probe analyses, and scanning electron microscopy to examine four interspecific macropodid hybrids (Macropus rufogriseus x Macropus agilis). The parental complements share the same centric fusions relative to the presumed macropodid ancestral karyotype, but can be differentiated on the basis of heterochromatic content, M. rufogriseus having larger centromeres with large C-banding positive regions. All hybrids exhibited the same pattern of chromosomal instability and remodeling specifically within the centromeres derived from the maternal (M. rufogriseus) complement. This instability included amplification of a satellite repeat and a transposable element, changes in chromatin structure, and de novo whole-arm rearrangements. We discuss possible reasons and mechanisms for the centromeric instability and remodeling observed in all four macropodid hybrids.
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23
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Hoshi Y, Mori M, Matoba H, Tagashira N, Murata T, Plader W, Malepszy S. Chromosomal Polymorphism of Two Pickling Cucumbers (Cucumis sativus L.) Revealed by Fluorescent Staining with CMA and DAPI. CYTOLOGIA 2008. [DOI: 10.1508/cytologia.73.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Hideyuki Matoba
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University
| | | | - Wojciech Plader
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw Agricultural University
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw Agricultural University
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24
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Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J. Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 2007; 176:2055-67. [PMID: 17565939 PMCID: PMC1950613 DOI: 10.1534/genetics.107.074286] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 05/17/2007] [Indexed: 12/26/2022] Open
Abstract
Polyploidy is remarkably common in the plant kingdom and polyploidization is a major driving force for plant genome evolution. Polyploids may contain genomes from different parental species (allopolyploidy) or include multiple sets of the same genome (autopolyploidy). Genetic and epigenetic changes associated with allopolyploidization have been a major research subject in recent years. However, we know little about the genetic impact imposed by autopolyploidization. We developed a synthetic autopolyploid series in potato (Solanum phureja) that includes one monoploid (1x) clone, two diploid (2x) clones, and one tetraploid (4x) clone. Cell size and organ thickness were positively correlated with the ploidy level. However, the 2x plants were generally the most vigorous and the 1x plants exhibited less vigor compared to the 2x and 4x individuals. We analyzed the transcriptomic variation associated with this autopolyploid series using a potato cDNA microarray containing approximately 9000 genes. Statistically significant expression changes were observed among the ploidies for approximately 10% of the genes in both leaflet and root tip tissues. However, most changes were associated with the monoploid and were within the twofold level. Thus, alteration of ploidy caused subtle expression changes of a substantial percentage of genes in the potato genome. We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration.
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Affiliation(s)
- Robert M Stupar
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
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25
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Comparative analysis of A, B, C and D genomes in the genus Oryza with C 0 t-1 DNA of C genome. CHINESE SCIENCE BULLETIN-CHINESE 2006. [DOI: 10.1007/s11434-006-2049-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Kao FI, Cheng YY, Chow TY, Chen HH, Liu SM, Cheng CH, Chung MC. An integrated map of Oryza sativa L. chromosome 5. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:891-902. [PMID: 16365756 DOI: 10.1007/s00122-005-0191-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 11/30/2005] [Indexed: 05/05/2023]
Abstract
The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.
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Affiliation(s)
- Fang-I Kao
- Institute of Plant and Microbial Biology, Academia Sinica, 115 Taipei, Taiwan, Republic of China
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27
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Haizel T, Lim YK, Leitch AR, Moore G. Molecular analysis of holocentric centromeres of Luzula species. Cytogenet Genome Res 2005; 109:134-43. [PMID: 15753569 DOI: 10.1159/000082392] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 11/20/2003] [Indexed: 11/19/2022] Open
Abstract
Luzula spp, like the rest of the members of the Juncaceae family, have holocentric chromosomes. Using the rice 155-bp centromeric tandem repeat sequence (RCS2) as a probe, we have isolated and characterized a 178-bp tandem sequence repeat (LCS1) from Luzula nivea. The LCS1 sequence is present in all Luzula species tested so far (except L. pilosa) and like other satellite repeats found in heterochromatin, the cytosine residues are methylated within the LCS1 repeats. Using fluorescent in situ hybridization (FISH) experiments we have shown that there are at least 5 large clusters of LCS1 sequences distributed at heterochromatin regions along each of the 12 chromosomes of L. nivea. We have shown that a centromeric antibody Skp1 co-localizes with these heterochromatin regions and with the LCS1 sequences. This suggests that the LCS1 sequences are part of regions which function as centromeres on these holocentric chromosomes. Furthermore, using the BrdU assay to identify replication sites, we have shown that these heterochromatin sites containing LCS1 associate when being replicated in root interphase nuclei. Our results also show premeiotic chromosome association during anther development as indicated by single-copy BAC in situ and the presence of fewer LCS1 containing heterochromatin sites in these cells.
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Affiliation(s)
- T Haizel
- Crop Genetics Dept, John Innes Centre, Colney Lane, Norwich, UK
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28
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Koo DH, Choi HW, Cho J, Hur Y, Bang JW. A high-resolution karyotype of cucumber (Cucumis sativus L. 'Winter Long') revealed by C-banding, pachytene analysis, and RAPD-aided fluorescence in situ hybridization. Genome 2005; 48:534-40. [PMID: 16121249 DOI: 10.1139/g04-128] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using molecular cytogenetic DNA markers, C-banding, pachytene analysis, and fluorescence in situ hybridization (FISH), a high-resolution karyotype was established in the cucumber. C-banding showed distinct hetero chro matic bands on the pericentromeric, telomeric, and intercalary regions of the chromosomes. The C-banding patterns were also consistent with the morphology of 4'-6-diamino-2-phenylindole dihydrochloride (DAPI)-stained pachytene chro mosomes. Two repetitive DNA fragments, CsRP1 and CsRP2, were obtained by PCR and localized on the mitotic metaphase and meiotic pachytene chromosomes. CsRP1 was detected on the pericentromeric heterochromatic regions of all chromosomes, except chromosome 1. CsRP2 was detected on 5 (chromosomes 1, 2, 3, 4, and 7) of 7 chromosomes. All homologous chromosome pairs could be distinguished by FISH using 2 RAPD markers. This is the first report on molecular karyotyping of mitotic and meiotic spreads of cucumber.Key words: Cucumis sativus, C-banding, FISH, karyotype, pachytene, RAPD marker, rDNA.
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Affiliation(s)
- Dal-Hoe Koo
- School of Bioscience and Biotechnology, Chungnam National University, Korea
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29
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Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J. Sequencing of a rice centromere uncovers active genes. Nat Genet 2004; 36:138-45. [PMID: 14716315 DOI: 10.1038/ng1289] [Citation(s) in RCA: 372] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 12/11/2003] [Indexed: 11/09/2022]
Abstract
Centromeres are the last frontiers of complex eukaryotic genomes, consisting of highly repetitive sequences that resist mapping, cloning and sequencing. The centromere of rice Chromosome 8 (Cen8) has an unusually low abundance of highly repetitive satellite DNA, which allowed us to determine its sequence. A region of approximately 750 kb in Cen8 binds rice CENH3, the centromere-specific H3 histone. CENH3 binding is contained within a larger region that has abundant dimethylation of histone H3 at Lys9 (H3-Lys9), consistent with Cen8 being embedded in heterochromatin. Fourteen predicted and at least four active genes are interspersed in Cen8, along with CENH3 binding sites. The retrotransposons located in and outside of the CENH3 binding domain have similar ages and structural dynamics. These results suggest that Cen8 may represent an intermediate stage in the evolution of centromeres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays.
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Affiliation(s)
- Kiyotaka Nagaki
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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30
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Cheng Z, Buell CR, Wing RA, Jiang J. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 2003; 10:379-87. [PMID: 12296520 DOI: 10.1023/a:1016849618707] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fluorescence in-situ hybridization (FISH) is a quick and affordable approach to map DNA sequences to specific chromosomal regions. Although FISH is one of the most important physical mapping techniques, research on the resolution of FISH on different cytological targets is scarce in plants. In this study, we report the resolution of FISH mapping on mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers in rice. A majority of the FISH signals derived from bacterial artificial chromosome (BAC) clones separated by approximately 1 Mb of DNA cannot be resolved on mitotic prometaphase chromosomes. In contrast, the relative positions of closely linked or even partially overlapping BAC clones can be resolved on a euchromatic region of rice chromosome 10 at the early pachytene stage. The resolution of pachytene FISH is dependent on early or late pachytene stages and also on the location of the DNA probes in the euchromatic or heterochromatic regions. We calibrated the fiber-FISH technique in rice using seven sequenced BAC clones. The average DNA extension was 3.21 kb/microm among the seven BAC clones. Fiber-FISH results derived from a BAC contig that spanned 1 Mb DNA matched remarkably to the sequencing data, demonstrating the high resolution of this technique in cytological mapping.
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Affiliation(s)
- Zhukuan Cheng
- Department of Horticulture, University of Wisconsin-Madison, 53706, USA
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Stupar RM, Song J, Tek AL, Cheng Z, Dong F, Jiang J. Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. Genetics 2002; 162:1435-44. [PMID: 12454086 PMCID: PMC1462313 DOI: 10.1093/genetics/162.3.1435] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S.25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.
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Affiliation(s)
- Robert M Stupar
- Department of Horticulture, University of Wisconsin, Madison 53706, USA
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Cheng Z, Buell CR, Wing RA, Gu M, Jiang J. Toward a cytological characterization of the rice genome. Genome Res 2001; 11:2133-41. [PMID: 11731505 PMCID: PMC311230 DOI: 10.1101/gr.194601] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rice (Oryza sativa L.) will be the first major crop, as well as the first monocot plant species, to be completely sequenced. Integration of DNA sequence-based maps with cytological maps will be essential to fully characterize the rice genome. We have isolated a set of 24 chromosomal arm-specific bacterial artificial chromosomes to facilitate rice chromosome identification. A standardized rice karyotype was constructed using meiotic pachytene chromosomes of O. sativa spp. japonica rice var. Nipponbare. This karyotype is anchored by centromere-specific and chromosomal arm-specific cytological landmarks and is fully integrated with the most saturated rice genetic linkage maps in which Nipponbare was used as one of the mapping parents. An ideogram depicting the distribution of heterochromatin in the rice genome was developed based on the patterns of 4',6-diamidino-2-phenylindole staining of the Nipponbare pachytene chromosomes. The majority of the heterochromatin is distributed in the pericentric regions with some rice chromosomes containing a significantly higher proportion of heterochromatin than other chromosomes. We showed that pachytene chromosome-based fluorescence in situ hybridization analysis is the most effective approach to integrate DNA sequences with euchromatic and heterochromatic features.
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Affiliation(s)
- Z Cheng
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J. High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 2001; 157:1749-57. [PMID: 11290728 PMCID: PMC1461616 DOI: 10.1093/genetics/157.4.1749] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Large-scale physical mapping has been a major challenge for plant geneticists due to the lack of techniques that are widely affordable and can be applied to different species. Here we present a physical map of rice chromosome 10 developed by fluorescence in situ hybridization (FISH) mapping of bacterial artificial chromosome (BAC) clones on meiotic pachytene chromosomes. This physical map is fully integrated with a genetic linkage map of rice chromosome 10 because each BAC clone is anchored by a genetically mapped restriction fragment length polymorphism marker. The pachytene chromosome-based FISH mapping shows a superior resolving power compared to the somatic metaphase chromosome-based methods. The telomere-centromere orientation of DNA clones separated by 40 kb can be resolved on early pachytene chromosomes. Genetic recombination is generally evenly distributed along rice chromosome 10. However, the highly heterochromatic short arm shows a lower recombination frequency than the largely euchromatic long arm. Suppression of recombination was found in the centromeric region, but the affected region is far smaller than those reported in wheat and barley. Our FISH mapping effort also revealed the precise genetic position of the centromere on chromosome 10.
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Affiliation(s)
- Z Cheng
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
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