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Serrano-León IM, Prieto P, Aguilar M. Telomere and subtelomere high polymorphism might contribute to the specificity of homologous recognition and pairing during meiosis in barley in the context of breeding. BMC Genomics 2023; 24:642. [PMID: 37884878 PMCID: PMC10601145 DOI: 10.1186/s12864-023-09738-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
Barley (Hordeum vulgare) is one of the most popular cereal crops globally. Although it is a diploid species, (2n = 2x = 14) the study of its genome organization is necessary in the framework of plant breeding since barley is often used in crosses with other cereals like wheat to provide them with advantageous characters. We already have an extensive knowledge on different stages of the meiosis, the cell division to generate the gametes in species with sexual reproduction, such as the formation of the synaptonemal complex, recombination, and chromosome segregation. But meiosis really starts with the identification of homologous chromosomes and pairing initiation, and it is still unclear how chromosomes exactly choose a partner to appropriately pair for additional recombination and segregation. In this work we present an exhaustive molecular analysis of both telomeres and subtelomeres of barley chromosome arms 2H-L, 3H-L and 5H-L. As expected, the analysis of multiple features, including transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots, G4 quadruplexes, genes and targeted sequence motifs for key DNA-binding proteins, revealed a high degree of variability both in telomeres and subtelomeres. The molecular basis for the specificity of homologous recognition and pairing occurring in the early chromosomal interactions at the start of meiosis in barley may be provided by these polymorphisms. A more relevant role of telomeres and most distal part of subtelomeres is suggested.
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Affiliation(s)
- I M Serrano-León
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain
| | - P Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal S/N., Campus Alameda del Obispo, 14004, Córdoba, Spain.
| | - M Aguilar
- Área de Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, Edif. C4, 3ª Planta, Córdoba, Spain
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2
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Huang X. A complete telomere-to-telomere assembly provides new reference genome for rice. MOLECULAR PLANT 2023; 16:1370-1372. [PMID: 37592749 DOI: 10.1016/j.molp.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Affiliation(s)
- Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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3
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Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu J, Wang K, Wang C, Xin B, Zhao H, Song W, Hufford MB, Schnable JC, Jin W, Lai J. A complete telomere-to-telomere assembly of the maize genome. Nat Genet 2023:10.1038/s41588-023-01419-6. [PMID: 37322109 DOI: 10.1038/s41588-023-01419-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of genomic research. Through generating deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads, we report here a complete genome assembly of maize with each chromosome entirely traversed in a single contig. The 2,178.6 Mb T2T Mo17 genome with a base accuracy of over 99.99% unveiled the structural features of all repetitive regions of the genome. There were several super-long simple-sequence-repeat arrays having consecutive thymine-adenine-guanine (TAG) tri-nucleotide repeats up to 235 kb. The assembly of the entire nucleolar organizer region of the 26.8 Mb array with 2,974 45S rDNA copies revealed the enormously complex patterns of rDNA duplications and transposon insertions. Additionally, complete assemblies of all ten centromeres enabled us to precisely dissect the repeat compositions of both CentC-rich and CentC-poor centromeres. The complete Mo17 genome represents a major step forward in understanding the complexity of the highly recalcitrant repetitive regions of higher plant genomes.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Zijian Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Wei Huang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Junpeng Shi
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Tong Li
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jiang Hu
- Grandomics Biosciences, Wuhan, P. R. China
| | - Kai Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Chao Wang
- Grandomics Biosciences, Wuhan, P. R. China
| | - Beibei Xin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Weiwei Jin
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, P. R. China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, P. R. China.
- Sanya Institute of China Agricultural University, Sanya, P. R. China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, P. R. China.
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4
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Guo H, Cui Y, Huang L, Ge L, Xu X, Xue D, Tang M, Zheng J, Yi Y, Chen L. The RNA binding protein OsLa influences grain and anther development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1397-1414. [PMID: 35322500 DOI: 10.1111/tpj.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
La proteins are found widely in eukaryotes and play a variety of vital roles. AtLa1 has been identified as an La protein that is necessary for embryogenesis in Arabidopsis; however, the existence and biological functions of La proteins in rice (Oryza sativa L.) remain unclear. In this study, we identified and characterized two La proteins in rice that are homologous to AtLa1 and named them OsLa1 and OsLa2. Both the OsLa1 and OsLa2 genes encode RNA-binding proteins with an La domain and two RNA-binding domains. Mutant OsLa1 reduced grain length and pollen fertility, whereas OsLa1 overexpression caused the opposite phenotypes. Further experiments indicated that OsLa1 modulates grain size by influencing cell expansion. Interestingly, mutant OsLa2 resulted in thin grains with decreased weight and a low seed-setting rate. We also found that OsLa1 interacted with OsLa2 and that both OsLa1 and OsLa2 interacted with OseIF6.1, a eukaryotic translation initiation factor involved in ribosome biogenesis. In addition, OsLa1 was able to bind to OseIF6.1 mRNA to modulate its expression. Complete OseIF6.1 knockout caused lethality and OseIF6.1/oseif6.1 heterozygous plants displayed low fertility and low seed setting. Together, our results enrich our knowledge of the role of La proteins in rice growth and development, as well as the relationship between La and eIF6 in rice.
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Affiliation(s)
- Hongming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Linjuan Huang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Li Ge
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaorong Xu
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Danyang Xue
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Jingsheng Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Science, Guizhou Normal University, Guiyang, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
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Gao D, Nascimento EFMB, Leal-Bertioli SCM, Abernathy B, Jackson SA, Araujo ACG, Bertioli DJ. TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.). Chromosome Res 2022; 30:77-90. [DOI: 10.1007/s10577-022-09684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/03/2022]
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Fu R, Wang C, Shen H, Zhang J, Higgins JD, Liang W. Rice OsBRCA2 Is Required for DNA Double-Strand Break Repair in Meiotic Cells. FRONTIERS IN PLANT SCIENCE 2020; 11:600820. [PMID: 33304374 PMCID: PMC7701097 DOI: 10.3389/fpls.2020.600820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/27/2020] [Indexed: 06/06/2023]
Abstract
The mammalian BREAST CANCER 2 (BRCA2) gene is a tumor suppressor that plays a crucial role in DNA repair and homologous recombination (HR). Here, we report the identification and characterization of OsBRCA2, the rice orthologue of human BRCA2. Osbrca2 mutant plants exhibit normal vegetative growth but experience complete male and female sterility as a consequence of severe meiotic defects. Pairing, synapsis and recombination are impaired in osbrca2 male meiocytes, leading to chromosome entanglements and fragmentation. In the absence of OsBRCA2, localization to the meiotic chromosome axes of the strand-invasion proteins OsRAD51 and OsDMC1 is severely reduced and in vitro OsBRCA2 directly interacts with OsRAD51 and OsDMC1. These results indicate that OsBRCA2 is essential for facilitating the loading of OsRAD51 and OsDMC1 onto resected ends of programmed double-strand breaks (DSB) during meiosis to promote single-end invasions of homologous chromosomes and accurate recombination. In addition, treatment of osbrca2-1 seedlings with mitomycin C (MMC) led to hypersensitivity. As MMC is a genotoxic agent that creates DNA lesions in the somatic cells that can only be repaired by HR, these results suggest that OsBRCA2 has a conserved role in DSB repair and HR in rice.
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Affiliation(s)
- Ruifeng Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Shen
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - James D. Higgins
- Department of Genetics and Genome Biology, University of Leicester,Leicester, United Kingdom
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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7
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Aguilar M, Prieto P. Sequence analysis of wheat subtelomeres reveals a high polymorphism among homoeologous chromosomes. THE PLANT GENOME 2020; 13:e20065. [PMID: 33029942 DOI: 10.1002/tpg2.20065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 05/23/2023]
Abstract
Bread wheat, Triticum aestivum L., is one of the most important crops in the world. Understanding its genome organization (allohexaploid; AABBDD; 2n = 6x = 42) is essential for geneticists and plant breeders. Particularly, the knowledge of how homologous chromosomes (equivalent chromosomes from the same genome) specifically recognize each other to pair at the beginning of meiosis, the cellular process to generate gametes in sexually reproducing organisms, is fundamental for plant breeding and has a big influence on the fertility of wheat plants. Initial homologous chromosome interactions contribute to specific recognition and pairing between homologues at the onset of meiosis. Understanding the molecular basis of these critical processes can help to develop genetic tools in a breeding context to promote interspecific chromosome associations in hybrids or interspecific genetic crosses to facilitate the transfer of desirable agronomic traits from related species into a crop like wheat. The terminal regions of chromosomes, which include telomeres and subtelomeres, participate in chromosome recognition and pairing. We present a detailed molecular analysis of subtelomeres of wheat chromosome arms 1AS, 4AS, 7AS, 7BS and 7DS. Results showed a high polymorphism in the subtelomeric region among homoeologues (equivalent chromosomes from related genomes) for all the features analyzed, including genes, transposable elements, repeats, GC content, predicted CpG islands, recombination hotspots and targeted sequence motifs for relevant DNA-binding proteins. These polymorphisms might be the molecular basis for the specificity of homologous recognition and pairing in initial chromosome interactions at the beginning of meiosis in wheat.
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Affiliation(s)
- Miguel Aguilar
- Área de Fisiología Vegetal. Universidad de Córdoba. Campus de Rabanales, edif. C4, 3a planta, Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4084, Córdoba, 14080, Spain
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8
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Sultana N, Menzel G, Heitkam T, Kojima KK, Bao W, Serçe S. Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes. Genes (Basel) 2020; 11:E527. [PMID: 32397417 PMCID: PMC7290377 DOI: 10.3390/genes11050527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.
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Affiliation(s)
- Nusrat Sultana
- Faculty of Life and Earth Sciences, Jagannath University, Dhaka 1100, Bangladesh
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Gerhard Menzel
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany; (G.M.); (T.H.)
| | - Kenji K. Kojima
- Genetic Information Research Institute, Cupertino, CA 95014, USA; (K.K.K.); (W.B.)
| | - Weidong Bao
- Genetic Information Research Institute, Cupertino, CA 95014, USA; (K.K.K.); (W.B.)
| | - Sedat Serçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey;
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9
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Liu Y, Liu Z, Wei Y, Wang Y, Shuang J, Peng R. Cloning and preliminary verification of telomere-associated sequences in upland cotton. COMPARATIVE CYTOGENETICS 2020; 14:183-195. [PMID: 32308926 PMCID: PMC7154043 DOI: 10.3897/compcytogen.v14i2.49391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Telomeres are structures enriched in repetitive sequences at the end of chromosomes. In this study, using the telomere primer AA(CCCTAAA)3CCC for the single primer PCR, two DNA sequences were obtained from Gossypium hirsutum (Linnaeus, 1753) accession (acc.) TM-1. Sequence analysis showed that the two obtained sequences were all rich in A/T base, which was consistent with the characteristic of the telomere-associated sequence (TAS). They were designated as GhTAS1 and GhTAS2 respectively. GhTAS1 is 489 bp long, with 57.6% of A/T, and GhTAS2 is 539 bp long, with 63.9% of A/T. Fluorescence in situ hybridization results showed that both of the cloned TASs were located at the ends of the partial chromosomes of G. hirsutum, with the strong signals, which further confirmed that GhTAS1 and GhTAS2 were telomere-associated sequences including highly tandemly repetitive sequences. Results of blast against the assembled genome of G. hirsutum showed that GhTAS sequences may be missed on some assembled chromosomes. The results provide important evidence for the evaluation of the integrity of assembled chromosome end sequences, and will also contribute to the further perfection of the draft genomes of cotton.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
| | - Yanjun Wang
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
| | - Jiaran Shuang
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, 455000, ChinaAnyang Institute of TechnologyAnyang CityChina
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Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
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11
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Zhang Q, Liang Z, Cui X, Ji C, Li Y, Zhang P, Liu J, Riaz A, Yao P, Liu M, Wang Y, Lu T, Yu H, Yang D, Zheng H, Gu X. N 6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses. MOLECULAR PLANT 2018; 11:1492-1508. [PMID: 30448535 DOI: 10.1016/j.molp.2018.11.005] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/03/2018] [Accepted: 11/11/2018] [Indexed: 05/23/2023]
Abstract
N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.
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Affiliation(s)
- Qian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhe Liang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Xuean Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Yun Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingrong Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pu Yao
- Biomarker Technologies, Beijing 101300, China
| | - Min Liu
- Biomarker Technologies, Beijing 101300, China
| | - Yunpeng Wang
- Institute of Clinical Medicine, University of Oslo, Oslo 0450, Norway
| | - Tiegang Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Donglei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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12
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Matsumoto T, Wu J, Itoh T, Numa H, Antonio B, Sasaki T. The Nipponbare genome and the next-generation of rice genomics research in Japan. RICE (NEW YORK, N.Y.) 2016; 9:33. [PMID: 27447712 PMCID: PMC4958085 DOI: 10.1186/s12284-016-0107-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/03/2016] [Indexed: 05/28/2023]
Abstract
The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.
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Affiliation(s)
- Takashi Matsumoto
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takeshi Itoh
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Hisataka Numa
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Baltazar Antonio
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Present Address: National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Takuji Sasaki
- Nodai Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
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Lee WK, Cho MH. Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Nucleic Acids Res 2016; 44:4610-24. [PMID: 26857545 PMCID: PMC4889915 DOI: 10.1093/nar/gkw067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 01/13/2023] Open
Abstract
Telomeres are nucleoprotein complexes at the end of eukaryotic chromosomes. Many telomere-binding proteins bind to telomeric repeat sequences and further generate T-loops in animals. However, it is not clear if they regulate telomere organization using epigenetic mechanisms and how the epigenetic molecules are involved in regulating the telomeres. Here, we show direct interactions between the telomere-binding protein, AtTRB2 and histone deacetylases, HDT4 and HDA6, in vitro and in vivo AtTRB2 mediates the associations of HDT4 and HDA6 with telomeric repeats. Telomere elongation is found in AtTRB2, HDT4 and HDA6 mutants over generations, but also in met1 and cmt3 DNA methyltransferases mutants. We also characterized HDT4 as an Arabidopsis H3K27 histone deacetylase. HDT4 binds to acetylated peptides at residue K27 of histone H3 in vitro, and deacetylates this residue in vivo Our results suggest that AtTRB2 also has a role in the regulation of telomeric chromatin as a possible scaffold protein for recruiting the epigenetic regulators in Arabidopsis, in addition to its telomere binding and length regulation activity. Our data provide evidences that epigenetic molecules associate with telomeres by direct physical interaction with telomere-binding proteins and further regulate homeostasis of telomeres in Arabidopsis thaliana.
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Affiliation(s)
- Won Kyung Lee
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
| | - Myeon Haeng Cho
- Department of Systems Biology, Yonsei University, Seoul 03722, Republic of Korea
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Souza G, Vanzela ALL, Crosa O, Guerra M. Interstitial telomeric sites and Robertsonian translocations in species of Ipheion and Nothoscordum (Amaryllidaceae). Genetica 2016; 144:157-66. [PMID: 26869260 DOI: 10.1007/s10709-016-9886-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
Abstract
The genera Nothoscordum and Ipheion (Allioideae, Amaryllidaceae) are cytologically characterized by a dysploid series with variable numbers of metacentric and acrocentric chromosomes typical of karyotypes rearranged by Robertsonian translocations (RT). Since they have large chromosomes, low diploid numbers, and possess two telomeric motifs [the vertebrate-type (TTAGGG) n and the Arabidopsis-type (TTTAGGG) n ] they are suitable for investigating the occurrence and possible role of interstitial telomeric sites (ITS) associated with RT. We analyzed the distributions of telomeric sites in 12 species of Nothoscordum and Ipheion and found that both telomeric probes colocalized in all chromosome termini. Cloning and sequencing PCR products obtained using both telomeric primers simultaneously revealed long stretches of (TTAGGG) n and (TTTAGGG) n sequences together with degenerated telomeric sequences. Most acrocentric chromosomes have a 45S rDNA site at the terminal region of the short arms adjacent to the most distal telomeric sites. Telomeric signals were found at all chromosome ends, but ITS were also detected in a few proximal and subterminal regions in some Nothoscordum species. Although RT are common in this group of plants, our findings suggest that proximal positioning of telomeric motifs are not necessarily related to that kind of rearrangement. Rather, transposition of telomeric sequences followed by amplification, could better explain the presence of (TTAGGG) n and (TTTAGGG) n repeats at those sites. Furthermore, a few small interstitial sites found in some Nothoscordum species indicate that dispersion of these sequences was not restricted to the proximal region.
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Affiliation(s)
- Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Centro de Ciências Biológicas, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
| | - Andre L L Vanzela
- Laboratory of Cytogenetics and Plant Diversity, Department of General Biology, State University of Londrina, Londrina, Paraná, Brazil
| | - Orfeo Crosa
- Laboratory of Genetics, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Marcelo Guerra
- Laboratory of Plant Cytogenetics and Evolution, Centro de Ciências Biológicas, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
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Nelson ADL, Forsythe ES, Gan X, Tsiantis M, Beilstein MA. Extending the model of Arabidopsis telomere length and composition across Brassicaceae. Chromosome Res 2015; 22:153-66. [PMID: 24846723 DOI: 10.1007/s10577-014-9423-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Telomeres are repetitive TG-rich DNA elements essential for maintaining the stability of genomes and replicative capacity of cells in almost all eukaryotes. Most of what is known about telomeres in plants comes from the angiosperm Arabidopsis thaliana, which has become an important comparative model for telomere biology. Arabidopsis tolerates numerous insults to its genome, many of which are catastrophic or lethal in other eukaryotic systems such as yeast and vertebrates. Despite the importance of Arabidopsis in establishing a model for the structure and regulation of plant telomeres, only a handful of studies have used this information to assay components of telomeres from across land plants, or even among the closest relatives of Arabidopsis in the plant family Brassicaceae. Here, we determined how well Arabidopsis represents Brassicaceae by comparing multiple aspects of telomere biology in species that represent major clades in the family tree. Specifically, we determined the telomeric repeat sequence, measured bulk telomere length, and analyzed variation in telomere length on syntenic chromosome arms. In addition, we used a phylogenetic approach to infer the evolutionary history of putative telomere-binding proteins, CTC1, STN1, TEN1 (CST), telomere repeat-binding factor like (TRFL), and single Myb histone (SMH). Our analyses revealed conservation of the telomeric DNA repeat sequence, but considerable variation in telomere length among the sampled species, even in comparisons of syntenic chromosome arms. We also found that the single-stranded and double-stranded telomeric DNA-binding complexes CST and TRFL, respectively, differ in their pattern of gene duplication and loss. The TRFL and SMH gene families have undergone numerous duplication events, and these duplicate copies are often retained in the genome. In contrast, CST components occur as single-copy genes in all sampled genomes, even in species that experienced recent whole genome duplication events. Taken together, our results place the Arabidopsis model in the context of other species in Brassicaceae, making the family the best characterized plant group in regard to telomere architecture.
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Affiliation(s)
- Andrew D L Nelson
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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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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17
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Systematic application of DNA fiber-FISH technique in cotton. PLoS One 2013; 8:e75674. [PMID: 24086609 PMCID: PMC3785504 DOI: 10.1371/journal.pone.0075674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/09/2013] [Indexed: 01/16/2023] Open
Abstract
Fluorescence in situ hybridization on extended DNA (fiber-FISH) is a powerful tool in high-resolution physical mapping. To introduce this technique into cotton, we developed the technique and tested it by deliberately mapping of telomere and 5S rDNA. Results showed that telomere-length ranged from 0.80 kb to 37.86 kb in three species, G. hirsutum, G. herbaceum and G. arboreum. However, most of the telomeres (>91.0%) were below 10 kb. The length of 5S rDNA was revealed as 964 kb in G. herbaceum whereas, in G. arboreum, it was approximately three times longer (3.1 Mb). A fiber-FISH based immunofluorescence method was also described to assay the DNA methylation. Using this technique, we revealed that both telomere and 5S rDNA were methylated at different levels. In addition, we developed a BAC molecule-based fiber-FISH technique. Using this technique, we can precisely map BAC clones on each other and evaluated the size and location of overlapped regions. The development and application of fiber-FISH technique will facilitate high-resolution physical mapping and further directed sequencing projects for cotton.
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18
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Lee WK, Yun JH, Lee W, Cho MH. DNA-binding domain of AtTRB2 reveals unique features of a single Myb histone protein family that binds to both Arabidopsis- and human-type telomeric DNA sequences. MOLECULAR PLANT 2012; 5:1406-1408. [PMID: 22859734 DOI: 10.1093/mp/sss063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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Xu C, Cheng Z, Yu W. Construction of rice mini-chromosomes by telomere-mediated chromosomal truncation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:1070-1079. [PMID: 22268496 DOI: 10.1111/j.1365-313x.2012.04916.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Telomere truncation has been shown to be an efficient technology for the creation of mini-chromosomes that can be used as artificial chromosome platforms for genetic engineering. Artificial chromosome-based genetic engineering is considered to be superior to the existing techniques of randomized gene integration by Agrobacterium or biolistic-mediated genetic transformation. It organizes multiple transgenes as a unique genetic linkage block for subsequent manipulations in breeding. Telomere truncation technology relies on three components: the telomere sequence that mediates chromosomal truncation, a selection marker that allows the selection of transgenic events, and a site-specific recombination system that can be used to accept future genes into the mini-chromosome by gene targeting. These elements are usually pre-assembled before transformation, a process that is both time and labor consuming. We found in this research that the three elements could be mixed to transform plant cells in a biolistic transformation, and produced efficient chromosomal truncations and mini-chromosomes in rice. This system will allow rapid construction of mini-chromosomes with a flexible selection of resistant markers, site-specific recombination systems and other desirable elements. In addition, a rice telotrisomic line was used as the starting material for chromosomal truncations. Mini-chromosomes from the truncations of both the telocentric chromosome and other chromosomes were recovered. The mini-chromosomes remained stable during 2 years of subculture. The construction of mini-chromosomes in rice, an economically important crop, will provide a platform for future artificial chromosome-based genetic engineering of rice for stacking multiple genes.
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Affiliation(s)
- Chunhui Xu
- State Key Laboratory for Agrobiotechnology, Institute of Plant Molecular Biology and Agricultural Biotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
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20
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Peng R, Zhang T, Liu F, Ling J, Wang C, Li S, Zhang X, Wang Y, Wang K. Preparations of meiotic pachytene chromosomes and extended DNA fibers from cotton suitable for fluorescence in situ hybridization. PLoS One 2012; 7:e33847. [PMID: 22442728 PMCID: PMC3307766 DOI: 10.1371/journal.pone.0033847] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/18/2012] [Indexed: 12/02/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become one of the most important techniques applied in plant molecular cytogenetics. However, the application of this technique in cotton has lagged behind because of difficulties in chromosome preparation. The focus of this article was FISH performed not only on cotton pachytene chromosomes, but also on cotton extended DNA fibers. The cotton pollen mother cells (PMCs) instead of buds or anthers were directly digested in enzyme to completely breakdown the cell wall. Before the routine acetic acid treatment, PMCs were incubated in acetic acid and enzyme mixture to remove the cytoplasm and clear the background. The method of ice-cold Carnoy's solution spreading chromosome was adopted instead of nitrogen removed method to avoid chromosomes losing and fully stretch chromosome. With the above-improved steps, the high-quality well-differentiated pachytene chromosomes with clear background were obtained. FISH results demonstrated that a mature protocol of cotton pachytene chromosomes preparation was presented. Intact and no debris cotton nuclei were obtained by chopping from etiolation cotyledons instead of the conventional liquid nitrogen grinding method. After incubating the nuclei with nucleus lysis buffer on slide, the parallel and clear background DNA fibers were acquired along the slide. This method overcomes the twist, accumulation and fracture of DNA fibers compared with other methods. The entire process of DNA fibers preparation requires only 30 min, in contrast, it takes 3 h with routine nitrogen grinding method. The poisonous mercaptoethanol in nucleus lysis buffer is replaced by nonpoisonous dithiothreitol. PVP40 in nucleus isolation buffer is used to prevent oxidation. The probability of success in isolating nuclei for DNA fiber preparation is almost 100% tested with this method in cotton. So a rapid, safe, and efficient method for the preparation of cotton extended DNA fibers suitable for FISH was established.
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Affiliation(s)
- Renhai Peng
- State Key Laboratory of Cotton Biology, China and Cotton Research Institute of Chinese Academy of Agricultural Science, Anyang, Henan, China
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21
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Chow EWL, Morrow CA, Djordjevic JT, Wood IA, Fraser JA. Microevolution of Cryptococcus neoformans driven by massive tandem gene amplification. Mol Biol Evol 2012; 29:1987-2000. [PMID: 22334577 DOI: 10.1093/molbev/mss066] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The subtelomeric regions of organisms ranging from protists to fungi undergo a much higher rate of rearrangement than is observed in the rest of the genome. While characterizing these ~40-kb regions of the human fungal pathogen Cryptococcus neoformans, we have identified a recent gene amplification event near the right telomere of chromosome 3 that involves a gene encoding an arsenite efflux transporter (ARR3). The 3,177-bp amplicon exists in a tandem array of 2-15 copies and is present exclusively in strains with the C. neoformans var. grubii subclade VNI A5 MLST profile. Strains bearing the amplification display dramatically enhanced resistance to arsenite that correlates with the copy number of the repeat; the origin of increased resistance was verified as transport-related by functional complementation of an arsenite transporter mutant of Saccharomyces cerevisiae. Subsequent experimental evolution in the presence of increasing concentrations of arsenite yielded highly resistant strains with the ARR3 amplicon further amplified to over 50 copies, accounting for up to ~1% of the whole genome and making the copy number of this repeat as high as that seen for the ribosomal DNA. The example described here therefore represents a rare evolutionary intermediate-an array that is currently in a state of dynamic flux, in dramatic contrast to relatively common, static relics of past tandem duplications that are unable to further amplify due to nucleotide divergence. Beyond identifying and engineering fungal isolates that are highly resistant to arsenite and describing the first reported instance of microevolution via massive gene amplification in C. neoformans, these results suggest that adaptation through gene amplification may be an important mechanism that C. neoformans employs in response to environmental stresses, perhaps including those encountered during infection. More importantly, the ARR3 array will serve as an ideal model for further molecular genetic analyses of how tandem gene duplications arise and expand.
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Affiliation(s)
- Eve W L Chow
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
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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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Ishii K, Amanai Y, Kazama Y, Ikeda M, Kamada H, Kawano S. Analysis of BAC clones containing homologous sequences on the end of the Xq arm and on chromosome 7 in the dioecious plant Silene latifolia. Genome 2010; 53:311-20. [PMID: 20616862 DOI: 10.1139/g10-008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silene latifolia is a model dioecious plant with morphologically distinguishable XY sex chromosomes. The end of the Xq arm is quite different from that of the Yp arm, although both are located at opposite ends of their respective chromosomes relative to a pseudo-autosomal region. The Xq arm does not seem to originate from the same autosome as the Yp arm. Bacterial artificial chromosome clone #15B12 has an insert containing a 130-kb stretch in which a 313-bp satellite DNA is repeated 420 times. PCR with a single primer revealed that this 130-kb stretch consists of three reversals of the orientation of the satellite DNA. A non-long terminal repeat retroelement and two sequences that share homology with an Oryza sativa RING zinc finger and a putative Arabidopsis thaliana protein, respectively, were found in the sequences that flank the satellite DNA. Fluorescence in situ hybridization carried out using this low-copy region of #15B12 as a probe confirmed that these sequences originated from the X chromosome and that homologous sequences exist at the end of chromosome 7. The region distal to DD44X on the Xq arm is postulated to have recombined with a region containing satellite DNA on chromosome 7 during the process of sex chromosome evolution.
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Affiliation(s)
- Kotaro Ishii
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8562, Japan
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Evtushenko EV, Vershinin AV. Heterogeneous organization of a tandem repeat family in subtelomeric heterochromatin of rye. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410090152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Schwartz SL, Farman ML. Systematic overrepresentation of DNA termini and underrepresentation of subterminal regions among sequencing templates prepared from hydrodynamically sheared linear DNA molecules. BMC Genomics 2010; 11:87. [PMID: 20122283 PMCID: PMC2824731 DOI: 10.1186/1471-2164-11-87] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 02/02/2010] [Indexed: 11/24/2022] Open
Abstract
Background Analysis of fungal genome sequence assemblies reveals that telomeres are poorly represented even though telomeric reads tend to be superabundant. We surmised that the problem might lie in the DNA shearing conditions used to create clone libraries for genome sequencing. Results A shotgun strategy was used to sequence and assemble circular and linear cosmid DNAs sheared using conditions typical for a genome project. The DNA sheared in circular form assembled into a single sequence contig. However, the linearized cosmid produced an incomplete assembly because the two DNA termini, though greatly overrepresented in the clone library used for sequencing, were separated from neighboring sequences by gaps of ~1.4 and 1.8 kb. These gap sizes were reduced, but not eliminated, by shearing the linear cosmid into smaller fragments. Mapping of shearing breakpoints revealed a paucity of breaks in the subterminal regions of the linearized cosmid and also near chromosome ends of the fungus Neurospora crassa. Conclusion Together, our data indicate that the ends of linear DNA molecules are recalcitrant to hydrodynamic shearing. We propose that this causes DNA termini to be overrepresented in the resulting fragment population but ultimately prevents their incorporation into sequence assemblies.
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Affiliation(s)
- Sherri L Schwartz
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA.
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Ohmido N, Fukui K, Kinoshita T. Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:103-16. [PMID: 20154468 PMCID: PMC3417561 DOI: 10.2183/pjab.86.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 01/04/2010] [Indexed: 05/28/2023]
Abstract
Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.
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Affiliation(s)
- Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.
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Salina EA, Sergeeva EM, Adonina IG, Shcherban AB, Afonnikov DA, Belcram H, Huneau C, Chalhoub B. Isolation and sequence analysis of the wheat B genome subtelomeric DNA. BMC Genomics 2009; 10:414. [PMID: 19732459 PMCID: PMC2756281 DOI: 10.1186/1471-2164-10-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 09/05/2009] [Indexed: 12/17/2022] Open
Abstract
Background Telomeric and subtelomeric regions are essential for genome stability and regular chromosome replication. In this work, we have characterized the wheat BAC (bacterial artificial chromosome) clones containing Spelt1 and Spelt52 sequences, which belong to the subtelomeric repeats of the B/G genomes of wheats and Aegilops species from the section Sitopsis. Results The BAC library from Triticum aestivum cv. Renan was screened using Spelt1 and Spelt52 as probes. Nine positive clones were isolated; of them, clone 2050O8 was localized mainly to the distal parts of wheat chromosomes by in situ hybridization. The distribution of the other clones indicated the presence of different types of repetitive sequences in BACs. Use of different approaches allowed us to prove that seven of the nine isolated clones belonged to the subtelomeric chromosomal regions. Clone 2050O8 was sequenced and its sequence of 119 737 bp was annotated. It is composed of 33% transposable elements (TEs), 8.2% Spelt52 (namely, the subfamily Spelt52.2) and five non-TE-related genes. DNA transposons are predominant, making up 24.6% of the entire BAC clone, whereas retroelements account for 8.4% of the clone length. The full-length CACTA transposon Caspar covers 11 666 bp, encoding a transposase and CTG-2 proteins, and this transposon accounts for 40% of the DNA transposons. The in situ hybridization data for 2050O8 derived subclones in combination with the BLAST search against wheat mapped ESTs (expressed sequence tags) suggest that clone 2050O8 is located in the terminal bin 4BL-10 (0.95-1.0). Additionally, four of the predicted 2050O8 genes showed significant homology to four putative orthologous rice genes in the distal part of rice chromosome 3S and confirm the synteny to wheat 4BL. Conclusion Satellite DNA sequences from the subtelomeric regions of diploid wheat progenitor can be used for selecting the BAC clones from the corresponding regions of hexaploid wheat chromosomes. It has been demonstrated for the first time that Spelt52 sequences were involved in the evolution of terminal regions of common wheat chromosomes. Our research provides new insights into the microcollinearity in the terminal regions of wheat chromosomes 4BL and rice chromosome 3S.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, pr, Lavrentieva 10, Novosibirsk, 630090, Russia.
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Li J, Yang F, Zhu J, He S, Li L. Characterization of a tandemly repeated subtelomeric sequence with inverted telomere repeats in maize. Genome 2009; 52:286-93. [PMID: 19234557 DOI: 10.1139/g09-005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this study, two complementary telomere primers were applied to a single-primer PCR. A clear amplification band was obtained with one primer, while a smear pattern was seen with the other primer. Sequence analysis of the isolated clones from this specific amplification band revealed that a 412 bp clone designated as MTAS1 shared high homology with a reported subtelomeric sequence (382 bp) from maize (Zea mays L.), which indicated that this clone was possibly present at subtelomeric regions. The clone MTAS1 displayed a novel structural feature flanked by the forward and inverted telomere repeats. Southern hybridization revealed a ladder of hybridization bands, suggesting that MTAS1 was a tandemly repeated sequence. Fluorescence in situ hybridization results showed that the strong MTAS1 signals were present at the ends of short arms of several long chromosomes, confirming that MTAS1 was a subtelomeric sequence and the high brightness of signals further indicated this cloned sequence was a highly and tandemly repetitive sequence in maize. Fluorescence in situ hybridization with telomeric DNA and MTAS1 as probes on metaphase chromosomes and extended genomic DNA fibers showed that hybridization signals of this clone located adjacent to or overlapped with signals of telomere tandem repeats distributed heterogeneously in subtelomeric regions of several chromosomes and even exhibited differences in two subtelomeres of a single chromosome.
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Affiliation(s)
- Jun Li
- Key Laboratory of MOE for Plant Development Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Shakirov EV, Salzberg SL, Alam M, Shippen DE. Analysis of Carica papaya Telomeres and Telomere-Associated Proteins: Insights into the Evolution of Telomere Maintenance in Brassicales. TROPICAL PLANT BIOLOGY 2008; 1:202-215. [PMID: 20664721 PMCID: PMC2909770 DOI: 10.1007/s12042-008-9018-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Telomeres are terminal regions of linear eukaryotic chromosomes that are critical for genome stability and continued cell proliferation. The draft assembly of the papaya genome provides an opportunity to analyze and compare the evolution of telomeric DNA sequence composition and telomere maintenance machinery in this and other organisms of the Brassicales Order, which includes Arabidopsis. Here we investigate telomere size and sequence variation at papaya chromosome ends. As with most other plant species, papaya telomeres consist of TTTAGGG repeats. However, in contrast to members of the closely related Brassicaceae family, telomeres in papaya are ~10-fold longer. Sequence analysis reveals that many centromereproximal telomere repeats in papaya harbor nucleotide substitutions and insertions of Gs and Ts. In contrast, we found very few N-to-C substitutions, and even fewer instances of nucleotide deletion, suggesting that a six-nucleotide telomere repeat is not well tolerated. The papaya genome encodes single-copy sequence homologues of several genes involved in telomere maintenance and chromosome end protection, including the Telomerase Reverse Transcriptase (TERT) and Protection Of Telomeres (POT1). Notably, unlike Arabidopsis, which encodes six Telomere Repeat binding Factor-like (TRFL) proteins that bind double-stranded telomere DNA, papaya appears to encode only two such proteins. Thus, the more streamlined genome of papaya will provide an excellent resource for comparative and functional analysis of telomeres in plants.
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Affiliation(s)
- E. V. Shakirov
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
| | - S. L. Salzberg
- Center for Bioinformatics and Computational Biology, and Department of Computer Science, University of Maryland, 3125 Biomolecular Sciences Bldg, College Park, MD 20742, USA
| | - M. Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, and Department of Microbiology, University of Hawaii, Honolulu, HI 96822, USA
| | - D. E. Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA,
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Fan C, Zhang Y, Yu Y, Rounsley S, Long M, Wing RA. The subtelomere of Oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. MOLECULAR PLANT 2008; 1:839-50. [PMID: 19825586 PMCID: PMC2902912 DOI: 10.1093/mp/ssn050] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 07/15/2008] [Indexed: 05/22/2023]
Abstract
Despite general observations of non-random genomic distribution of new genes, it is unclear whether or not new genes preferentially occur in certain genomic regions driven by related molecular mechanisms. Using 1.5 Mb of genomic sequences from short arms of chromosome 3 of Oryza glaberrima and O. punctata, we conducted a comparative genomic analysis with the reference O. sativa ssp. japonica genome. We identified a 60-kb segment located in the middle of the subtelomeric region of chromosome 3, which is unique to the species O. sativa. The region contained gene duplicates that occurred in Asian cultivated rice species that diverged from the ancestor of Asian and African cultivated rice one million years ago (MYA). For the 12 genes and one complete retrotransposon identified in this segment in O. sativa ssp. japonica, we searched for their parental genes. The high similarity between duplicated paralogs further supports the recent origination of these genes. We found that this segment was recently generated through multiple independent gene recombination and transposon insertion events. Among the 12 genes, we found that five had chimeric gene structures derived from multiple parental genes. Nine out of the 12 new genes seem to be functional, as suggested by Ka/Ks analysis and the presence of cDNA and/or MPSS data. Furthermore, for the eight transcribed genes, at least two genes could be classified as defense or stress response-related genes. Given these findings, and the fact that subtelomeres are associated with high rates of recombination and transcription, it is likely that subtelomeres may facilitate gene recombination and transposon insertions and serve as hot spots for new gene origination in rice genomes.
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Affiliation(s)
- Chuanzhu Fan
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Yong Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Steve Rounsley
- BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- To whom correspondence should be addressed. E-mail , fax 773-702-9740, tel. 773-702-0557. E-mail , fax 520-621-1259, tel. 520-626-9595
| | - Rod A. Wing
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- To whom correspondence should be addressed. E-mail , fax 773-702-9740, tel. 773-702-0557. E-mail , fax 520-621-1259, tel. 520-626-9595
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Zhang D, Yang Q, Ding Y, Cao X, Xue Y, Cheng Z. Cytological characterization of the tandem repetitive sequences and their methylation status in the Antirrhinum majus genome. Genomics 2008; 92:107-14. [PMID: 18559290 DOI: 10.1016/j.ygeno.2008.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 04/17/2008] [Accepted: 04/19/2008] [Indexed: 12/21/2022]
Abstract
Tandem repetitive sequences are DNA motifs common in the genomes of eukaryotic species and are often embedded in heterochromatic regions. In most eukaryotes, ribosomal genes, as well as centromeres and telomeres or subtelomeres, are associated with abundant tandem arrays of repetitive sequences and typically represent the final barriers to completion of whole-genome sequencing. The nature of these repeats makes it difficult to estimate their actual sizes. In this study, combining the two cytological techniques DNA fiber-FISH and pachytene chromosome FISH allowed us to characterize the tandem repeats distributed genome wide in Antirrhinum majus and identify four types of tandem repeats, 45S rDNA, 5S rDNA, CentA1, and CentA2, representing the major tandem repetitive components, which were estimated to have a total length of 18.50 Mb and account for 3.59% of the A. majus genome. FISH examination revealed that all the tandem repeats correspond to heterochromatic knobs along the pachytene chromosomes. Moreover, the methylation status of the tandem repeats was investigated in both somatic cells and pollen mother cells from anther tissues using an antibody against 5-methylcytosine combined with sequential FISH analyses. Our results showed that these repeats were hypomethylated in anther tissues, especially in the pollen mother cells at pachytene stage.
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Affiliation(s)
- Dongfen Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Beijing 100101, China
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Mizuno H, Wu J, Katayose Y, Kanamori H, Sasaki T, Matsumoto T. Characterization of chromosome ends on the basis of the structure of TrsA subtelomeric repeats in rice (Oryza sativa L.). Mol Genet Genomics 2008; 280:19-24. [PMID: 18392854 DOI: 10.1007/s00438-008-0341-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/24/2008] [Accepted: 03/26/2008] [Indexed: 11/27/2022]
Abstract
Subtelomeres contain species-specific repetitive sequences. We characterized rice chromosome ends on the basis of the structure of TrsA, a subtelomeric repetitive sequence of rice. Among the 24 chromosome arms, TrsA was arrayed in tandem on the ends of five: 5L, 6S, 8L, 9L, and 12L. TrsA sequences were arranged in discrete clusters of 3-106 copies in a chromosome-specific manner, instead of being distributed uniformly throughout the subtelomeric regions. The clusters were located at the distal-most end of the sequenced region in 5L, 6S, 8L, and 9L, but in 12L expressed genes were present distal to the clusters. Thus, rice subtelomeres are composed of discrete clusters of a TrsA-rich region and a gene-rich region with high transcriptional activity. Intra-chromosomal duplications have resulted in a striking degree of variation in the number and distribution of TrsAs, suggesting that the areas near the ends of the chromosomes are dynamic and variable.
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Affiliation(s)
- Hiroshi Mizuno
- National Institute of Agrobiological Sciences, 1-2, Kannondai 2-chome, Tsukuba, Ibaraki 305-8602, Japan.
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Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi IR, Nagamura Y, Matsumoto T, Murakami K, Matsubara KI, Carninci P, Hayashizaki Y, Kikuchi S. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One 2007; 2:e1235. [PMID: 18043742 PMCID: PMC2084198 DOI: 10.1371/journal.pone.0001235] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 10/30/2007] [Indexed: 01/11/2023] Open
Abstract
Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.
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Affiliation(s)
- Kouji Satoh
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Koji Doi
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Toshifumi Nagata
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Naoki Kishimoto
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kohji Suzuki
- Hitachi Software Engineering, Shinagawa-ku, Tokyo, Japan
| | - Yasuhiro Otomo
- Laboratory of Genome Sequencing and Analysis Group, Foundation for Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan
| | - Jun Kawai
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
- Genome Science Laboratory, RIKEN Wako Institute, Wako, Saitama, Japan
| | - Mari Nakamura
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Tomoko Hirozane-Kishikawa
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Saeko Kanagawa
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Takahiro Arakawa
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Juri Takahashi-Iida
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Noriko Ninomiya
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Daisuke Sasaki
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Shiro Fukuda
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Michihira Tagami
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
| | - Harumi Yamagata
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Kanako Kurita
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Kozue Kamiya
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Mayu Yamamoto
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Ari Kikuta
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Takahito Bito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Nahoko Fujitsuka
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Kazue Ito
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Kanamori
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, Japan
| | - Il-Ryong Choi
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Yoshiaki Nagamura
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Takashi Matsumoto
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kazuo Murakami
- Laboratory of Genome Sequencing and Analysis Group, Foundation for Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan
| | - Ken-ichi Matsubara
- Laboratory of Genome Sequencing and Analysis Group, Foundation for Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan
- Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan
| | - Piero Carninci
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
- Genome Science Laboratory, RIKEN Wako Institute, Wako, Saitama, Japan
| | - Yoshihide Hayashizaki
- Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan
- Genome Science Laboratory, RIKEN Wako Institute, Wako, Saitama, Japan
| | - Shoshi Kikuchi
- Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- * To whom correspondence should be addressed. E-mail:
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Gaut BS, Wright SI, Rizzon C, Dvorak J, Anderson LK. Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet 2007; 8:77-84. [PMID: 17173059 DOI: 10.1038/nrg1970] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA.
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Fujisawa M, Yamagata H, Kamiya K, Nakamura M, Saji S, Kanamori H, Wu J, Matsumoto T, Sasaki T. Sequence comparison of distal and proximal ribosomal DNA arrays in rice (Oryza sativa L.) chromosome 9S and analysis of their flanking regions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:419-28. [PMID: 16733757 DOI: 10.1007/s00122-006-0307-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 05/06/2006] [Indexed: 05/09/2023]
Abstract
Rice (Oryza sativa ssp. japonica cv. Nipponbare) harbors a ribosomal RNA gene (rDNA) cluster in the nucleolar-organizing region at the telomeric end of the short arm of chromosome 9. We isolated and sequenced two genomic clones carrying rice rDNA fragments from this region. The rice rDNA repeat units could be classified into three types based on length, which ranged from 7,928 to 8,934 bp. This variation was due to polymorphism in the number of 254-bp subrepeats in the intergenic spacer (IGS). Polymerase chain reaction (PCR) analysis suggested that the rDNA units in rice vary widely in length and that the copy number of the subrepeats in the IGS ranges from 1 to 12 in the rice genome. PCR and Southern blot analyses showed that most rDNA units have three intact and one truncated copies of the subrepeats in the IGS, and distal (telomere-side) rDNA units have more subrepeats than do proximal (centromere-side) ones. Both genomic clones we studied contained rDNA-flanking DNA sequences of either telomeric repeats (5'-TTTAGGG-3') or a chromosome-specific region, suggesting that they were derived from the distal or proximal end, respectively, of the rDNA cluster. A similarity search indicated that retrotransposons appeared more frequently in a 500-kb portion of the proximal rDNA-flanking region than in other subtelomeric regions or sequenced regions of the genome. This study reveals the repetitive nature of the telomeric end of the short arm of chromosome 9, which consists of telomeric repeats, an rDNA array, and a retrotransposon-rich chromosomal region.
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Affiliation(s)
- Masaki Fujisawa
- Rice Genome Research Program, National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, 305-8602, Japan
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