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Liu Y, Huang S, Han J, Hou C, Zheng D, Zhang Z, Wu J. Development and Molecular Cytogenetic Identification of a New Wheat- Psathyrostachys huashanica Keng Translocation Line Resistant to Powdery Mildew. FRONTIERS IN PLANT SCIENCE 2021; 12:689502. [PMID: 34163516 PMCID: PMC8215663 DOI: 10.3389/fpls.2021.689502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Psathyrostachys huashanica Keng, a wild relative of common wheat with many desirable traits, is an invaluable source of genetic material for wheat improvement. Few wheat-P. huashanica translocation lines resistant to powdery mildew have been reported. In this study, a wheat-P. huashanica line, E24-3-1-6-2-1, was generated via distant hybridization, ethyl methanesulfonate (EMS) mutagenesis, and backcross breeding. A chromosome karyotype of 2n = 44 was observed at the mitotic stage in E24-3-1-6-2-1. Genomic in situ hybridization (GISH) analysis revealed four translocated chromosomes in E24-3-1-6-2-1, and P. huashanica chromosome-specific marker analysis showed that the alien chromosome fragment was from the P. huashanica 4Ns chromosome. Moreover, fluorescence in situ hybridization (FISH) analysis demonstrated that reciprocal translocation had occurred between the P. huashanica 4Ns chromosome and the wheat 3D chromosome; thus, E24-3-1-6-2-1 carried two translocations: T3DS·3DL-4NsL and T3DL-4NsS. Translocation also occurred between wheat chromosomes 2A and 4A. At the adult stage, E24-3-1-6-2-1 was highly resistant to powdery mildew, caused by prevalent pathotypes in China. Further, the spike length, numbers of fertile spikelets, kernels per spike, thousand-kernel weight, and grain yield of E24-3-1-6-2-1 were significantly higher than those of its wheat parent 7182 and addition line 24-6-3-1. Thus, this translocation line that is highly resistant to powdery mildew and has excellent agronomic traits can be used as a novel promising germplasm for breeding resistant and high-yielding cultivars.
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Affiliation(s)
- Yuxiu Liu
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Shuhua Huang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jing Han
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Chenchen Hou
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Dasheng Zheng
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhengmao Zhang
- College of Agronomy, Northwest A&F University, Yangling, China
| | - Jun Wu
- College of Agronomy, Northwest A&F University, Yangling, China
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Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris). G3-GENES GENOMES GENETICS 2016; 6:2091-101. [PMID: 27185400 PMCID: PMC4938662 DOI: 10.1534/g3.116.028761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
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Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives. G3-GENES GENOMES GENETICS 2016; 6:1013-22. [PMID: 26865698 PMCID: PMC4825637 DOI: 10.1534/g3.115.024984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.
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Iwata-Otsubo A, Lin JY, Gill N, Jackson SA. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis. Chromosome Res 2016; 24:197-216. [PMID: 26758200 PMCID: PMC4856725 DOI: 10.1007/s10577-015-9515-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022]
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.
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Affiliation(s)
- Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.,Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jer-Young Lin
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Navdeep Gill
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
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5
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Multicolour interphase cytogenetics: 24 chromosome probes, 6 colours, 4 layers. Mol Cell Probes 2011; 25:199-205. [DOI: 10.1016/j.mcp.2011.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 07/19/2011] [Accepted: 08/16/2011] [Indexed: 11/18/2022]
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Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors. Genetics 2010; 187:37-49. [PMID: 21041557 DOI: 10.1534/genetics.110.122473] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two successive hybridizations allowed for routine identification of the corresponding homoeologous chromosomes between the A and C genomes of B. napus. When applied to the B. napus cultivar Stellar, we detected one chromosomal rearrangement relative to the parental karyotypes. This robust novel chromosomal painting technique will have biological applications for the understanding of chromosome pairing, homoeologous recombination, and genome evolution in the genus Brassica and will facilitate new applied breeding technologies that rely upon identification of chromosomes.
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Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:584-98. [PMID: 20525006 DOI: 10.1111/j.1365-313x.2010.04263.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 long terminal repeat-retrotransposon (LTR-RT) families comprising 32370 elements in soybean (Glycine max (L.) Merr.). Approximately 87% of these elements were located in recombination-suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that of chromosome arms (1.62). Further analysis revealed a significant positive correlation between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed seven Copia and five Gypsy evolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, a Copia lineage has been lost in soybean. Analysis of the physical association of LTR-RTs with centromere satellite repeats identified two putative centromere retrotransposon (CR) families of soybean, which were grouped into the CR (e.g. CRR and CRM) lineage found in grasses, indicating that the 'functional specification' of CR pre-dates the bifurcation of eudicots and monocots. However, a number of families of the CR lineage are not concentrated in centromeres, suggesting that their CR roles may now be defunct. Our data also suggest that the envelope-like genes in the putative Copia retrovirus-like family are probably derived from the Gypsy retrovirus-like lineage, and thus we propose the hypothesis of a single ancient origin of envelope-like genes in flowering plants.
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Affiliation(s)
- Jianchang Du
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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8
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Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMiguel P, Jiang N, Cheng Z, Wing RA, Jiang J, Jackson SA. A lineage-specific centromere retrotransposon in Oryza brachyantha. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:820-831. [PMID: 19702667 DOI: 10.1111/j.1365-313x.2009.04005.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.
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Affiliation(s)
- Dongying Gao
- Molecular and Evolutionary Genetics, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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9
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Staton SE, Ungerer MC, Moore RC. The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species. AMERICAN JOURNAL OF BOTANY 2009; 96:1646-1655. [PMID: 21622351 DOI: 10.3732/ajb.0800337] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The origin of new diploid, or homoploid, hybrid species is associated with rapid genomic restructuring in the hybrid neospecies. This mode of speciation has been best characterized in wild sunflower species in the genus Helianthus, where three homoploid hybrid species (H. anomalus, H. deserticola, and H. paradoxus) have independently arisen via ancient hybridization events between the same two parental species (H. annuus and H. petiolaris). Most previous work examining genomic restructuring in these sunflower hybrid species has focused on chromosomal rearrangements. However, the origin of all three homoploid hybrid sunflower species also is associated with massive proliferation events of Ty3/gypsy-like retrotransposons in the hybrid species' genomes. We compared the genomic organization of these elements in the parent species and two of the homoploid hybrid species using fluorescence in situ hybridization (FISH). We found a significant expansion of Ty3/gypsy-like retrotransposons confined to the pericentromeric regions of two hybrid sunflower species, H. deserticola and H. paradoxus. In contrast, we detected no significant increase in the frequency or extent of dispersed retrotransposon populations in the hybrid species within the resolution limits of our assay. We discuss the potential role that transposable element proliferation and localization plays in the evolution of homoploid hybrid species.
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Affiliation(s)
- S Evan Staton
- Miami University, Department of Botany, 316 Pearson Hall, Oxford, Ohio 45056 USA
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10
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Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NWG, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. PLANT PHYSIOLOGY 2008; 148:1740-59. [PMID: 18842825 PMCID: PMC2593655 DOI: 10.1104/pp.108.127902] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/06/2008] [Indexed: 05/18/2023]
Abstract
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
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Affiliation(s)
- Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
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11
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Tomita R, Murai J, Miura Y, Ishihara H, Liu S, Kubotera Y, Honda A, Hatta R, Kuroda T, Hamada H, Sakamoto M, Munemura I, Nunomura O, Ishikawa K, Genda Y, Kawasaki S, Suzuki K, Meksem K, Kobayashi K. Fine mapping and DNA fiber FISH analysis locates the tobamovirus resistance gene L3 of Capsicum chinense in a 400-kb region of R-like genes cluster embedded in highly repetitive sequences. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1107-1118. [PMID: 18663424 PMCID: PMC2755798 DOI: 10.1007/s00122-008-0848-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 07/11/2008] [Indexed: 05/26/2023]
Abstract
The tobamovirus resistance gene L(3) of Capsicum chinense was mapped using an intra-specific F2 population (2,016 individuals) of Capsicum annuum cultivars, into one of which had been introduced the C. chinense L(3) gene, and an inter-specific F2 population (3,391 individuals) between C. chinense and Capsicum frutescence. Analysis of a BAC library with an AFLP marker closely linked to L(3)-resistance revealed the presence of homologs of the tomato disease resistance gene I2. Partial or full-length coding sequences were cloned by degenerate PCR from 35 different pepper I2 homologs and 17 genetic markers were generated in the inter-specific combination. The L(3) gene was mapped between I2 homolog marker IH1-04 and BAC-end marker 189D23M, and located within a region encompassing two different BAC contigs consisting of four and one clones, respectively. DNA fiber FISH analysis revealed that these two contigs are separated from each other by about 30 kb. DNA fiber FISH results and Southern blotting of the BAC clones suggested that the L(3) locus-containing region is rich in highly repetitive sequences. Southern blot analysis indicated that the two BAC contigs contain more than ten copies of the I2 homologs. In contrast to the inter-specific F2 population, no recombinant progeny were identified to have a crossover point within two BAC contigs consisting of seven and two clones in the intra-specific F2 population. Moreover, distribution of the crossover points differed between the two populations, suggesting linkage disequilibrium in the region containing the L locus.
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Affiliation(s)
- R. Tomita
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - J. Murai
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Osaka 537-8511 Japan
| | - Y. Miura
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Nippon Flour Mills Co., Ltd, Central Laboratory, Atsugi, Kanagawa 243-0041 Japan
| | - H. Ishihara
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
- Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - S. Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
| | - Y. Kubotera
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - A. Honda
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - R. Hatta
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - T. Kuroda
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Crop Center, Niigata Agricultural Research Institute, Nagaoka, Niigata 940-0826 Japan
| | - H. Hamada
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- National Agricultural Research Center, Tsukuba, Ibaraki 305-8666 Japan
| | - M. Sakamoto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - I. Munemura
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - O. Nunomura
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - K. Ishikawa
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - Y. Genda
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - S. Kawasaki
- National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602 Japan
| | - K. Suzuki
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga 522-8533 Japan
| | - K. Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
| | - K. Kobayashi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
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12
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Hyper-phosphorylated retinoblastoma protein suppresses telomere elongation. Biosci Biotechnol Biochem 2008; 72:630-5. [PMID: 18256459 DOI: 10.1271/bbb.70715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Immortalized cell lines maintain telomeres by the expression of telomerase or by a mechanism designated alternative lengthening of telomeres (ALT). Although DNA polymerase alpha (pol-alpha) is reported to be required for telomere maintenance, the critical role of pol-alpha in telomere maintenance has not been firmly determined. We examined the role of retinoblastoma protein (pRb) and pol-alpha in the regulation of telomere length, using telomere-fiber FISH. Telomere length varied dependent on the intracellular abundance of pol-alpha or pRb in HeLa cells. A proportion of hyper-phosphorylated pRb (ppRb) molecules localized to sites of telomeric DNA replication in HeLa cells. Pol-alpha might thus contribute to telomere maintenance, and might be regulated by ppRb.
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Ammiraju JSS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:342-51. [PMID: 17764506 DOI: 10.1111/j.1365-313x.2007.03242.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.
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Affiliation(s)
- Jetty S S Ammiraju
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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14
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Jenkins G, Hasterok R. BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment. Nat Protoc 2007; 2:88-98. [PMID: 17401342 DOI: 10.1038/nprot.2006.490] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) with large genomic DNA inserts as probes (BAC 'landing') is a powerful means by which eukaryotic genomes can be physically mapped and compared. Here we report a BAC landing protocol that has been developed specifically for the weedy grass species Brachypodium distachyon, which has been adopted recently by the scientific community as an alternative model for the temperate cereals and grasses. The protocol describes the preparation of somatic and meiotic chromosome substrates for FISH, the labeling of BACs, a chromosome mapping strategy, empirical conditions for optimal in situ hybridization and stringency washing, the detection of probes and the capturing and processing of images. The expected outcome of the protocol is the specific assignment of BACs containing single-copy inserts to one of the five linkage groups of the genome of this species. Once somatic or meiotic material is available, the entire protocol can be completed in about 3 d. The protocol has been customized empirically for B. distachyon and its near relatives, but it can be adapted with minor modifications to diverse plant species.
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Affiliation(s)
- Glyn Jenkins
- Institute of Biological Sciences, University of Wales Aberystwyth, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK.
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Walling JG, Shoemaker R, Young N, Mudge J, Jackson S. Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 2006; 172:1893-900. [PMID: 16361231 PMCID: PMC1456260 DOI: 10.1534/genetics.105.051466] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 12/06/2005] [Indexed: 11/18/2022] Open
Abstract
Soybean has 20 chromosome pairs that are derived from at least two rounds of genomewide duplication or polyploidy events although, cytogenetically, soybean behaves like a diploid and has disomic inheritance for most loci. Genetically anchored genomic clones were used as probes for fluorescence in situ hybridization (FISH) to determine the level of postpolyploid chromosomal rearrangements and to integrate the genetic and physical maps to (1) assign linkage groups to specific chromosomes, (2) assess chromosomal structure, and (3) determine the distribution of recombination along the length of a chromosome. FISH mapping of seven putatively gene-rich BACs from linkage group L (chromosome 19) revealed that most of the genetic map correlates to the highly euchromatic long arm and that there is extensive homeology with another chromosome pair, although colinearity of some loci does appear to be disrupted. Moreover, mapping of BACs containing high-copy sequences revealed sequestration of high-copy repeats to the pericentromeric regions of this chromosome. Taken together, these data present a model of chromosome structure in a highly duplicated but diploidized eukaryote, soybean.
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Affiliation(s)
- Jason G Walling
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47906, USA
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Hall SE, Luo S, Hall AE, Preuss D. Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics 2005; 170:1913-27. [PMID: 15937135 PMCID: PMC1449784 DOI: 10.1534/genetics.104.038208] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Higher eukaryotic centromeres contain thousands of satellite repeats organized into tandem arrays. As species diverge, new satellite variants are homogenized within and between chromosomes, yet the processes by which particular sequences are dispersed are poorly understood. Here, we isolated and analyzed centromere satellites in plants separated from Arabidopsis thaliana by 5-20 million years, uncovering more rapid satellite divergence compared to primate alpha-satellite repeats. We also found that satellites derived from the same genomic locus were more similar to each other than satellites derived from disparate genomic regions, indicating that new sequence alterations were homogenized more efficiently at a local, rather than global, level. Nonetheless, the presence of higher-order satellite arrays, similar to those identified in human centromeres, indicated limits to local homogenization and suggested that sequence polymorphisms may play important functional roles. In two species, we defined more extensive polymorphisms, identifying physically separated and highly distinct satellite types. Taken together, these data show that there is a balance between plant satellite homogenization and the persistence of satellite variants. This balance could ultimately generate sufficient sequence divergence to cause mating incompatibilities between plant species, while maintaining adequate conservation within a species for centromere activity.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Base Sequence
- Centromere/genetics
- Chromatin Immunoprecipitation
- Consensus Sequence
- DNA, Plant/analysis
- DNA, Satellite/genetics
- DNA, Satellite/metabolism
- Fluorescein-5-isothiocyanate
- Fluorescent Antibody Technique, Direct
- Fluorescent Dyes
- Genome, Plant
- Heterochromatin/metabolism
- In Situ Hybridization, Fluorescence
- Indoles
- Microscopy, Fluorescence
- Molecular Sequence Data
- Phylogeny
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Sarah E Hall
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA
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