17 results on '"Piegu, B."'
Search Results
2. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza
- Author
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Jetty, S., Zuccolo, Andrea, Yu, Y., Song, X., Piegu, B., Chevalier, F., Walling, J., Ma, J., Talag, J., Brar, D., Sanmiguel, P., Jiang, N., Jackson, S., Panaud, O., Wing, R., Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Agronomy, Purdue University [West Lafayette], and Genomics Core Facility
- Subjects
[SDV]Life Sciences [q-bio] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2007
- Full Text
- View/download PDF
3. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
- Author
-
Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., Grigoriev, I. V., Worden, A. Z., Lee, J.-H., Mock, Thomas, Rouzé, P., Simmson, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, Uwe, Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van de Peer, Y., and Grigoriev, I. V.
- Published
- 2009
4. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes micromonas
- Author
-
Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., Grigoriev, I.V., Worden, Alexandra Z., Lee, J.-H., Mock, T., Rouzé, P., Simmons, M. P., Aerts, A. L., Allen, A. E., Cuvelier, M. L., Derelle, E., Everett, M. V., Foulon, E., Grimwood, J., Gundlach, H., Henrissat, B., Napoli, C., McDonald, S. M., Parker, M. S., Rombauts, S., Salamov, A., Von Dassow, P., Badger, J. H., Coutinho, P. M., Demir, E., Dubchak, I., Gentemann, C., Eikrem, W., Gready, J. E., John, U., Lanier, W., Lindquist, E. A., Lucas, S., Mayer, K. F. X., Moreau, H., Not, F., Otillar, R., Panaud, O., Pangilinan, J., Paulsen, I., Piegu, B., Poliakov, A., Robbens, S., Schmutz, J., Toulza, E., Wyss, T., Zelensky, A., Zhou, K., Armbrust, E. V., Bhattacharya, D., Goodenough, U. W., Van De Peer, Y., and Grigoriev, I.V.
- Abstract
Picoeukaryotes are a taxonomically diverse group of organism less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90 of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
- Published
- 2009
- Full Text
- View/download PDF
5. The Rice Annotation Project Database (RAP-DB): 2008 update
- Author
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Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J.-i., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y-C, Wei, F-J, Hsing, Y-i, Zhao, Q., Bin, H., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H-R, Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M., Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J.-i., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y-C, Wei, F-J, Hsing, Y-i, Zhao, Q., Bin, H., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H-R, Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., and Echeverria, M.
- Abstract
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
- Published
- 2008
6. RetrOryza: a database of the rice LTR-retrotransposons
- Author
-
Chaparro, C., primary, Guyot, R., additional, Zuccolo, A., additional, Piegu, B., additional, and Panaud, O., additional
- Published
- 2007
- Full Text
- View/download PDF
7. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice (Genome Research (2006) 16, (1262-1269))
- Author
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Piegu, B., Guyot, R., Picault, N., Roulin, A., Sanyal, A., Kim, H., Collura, K., Brar, D. S., Jackson, S., Rod Wing, and Panaud, O.
8. Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data.
- Author
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Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, Piegu B, Roulin A, Guiderdoni E, Delabastide M, McCombie R, and Panaud O
- Subjects
- Chromosome Mapping, Chromosomes, Plant, DNA, Plant genetics, Genetic Variation, Sequence Analysis, DNA, DNA Transposable Elements, Genome, Plant, Mutagenesis, Insertional, Oryza genetics
- Abstract
Transposable elements (TEs) are mobile entities that densely populate most eukaryotic genomes and contribute to both their structural and functional dynamics. However, most TE-related sequences in both plant and animal genomes correspond to inactive, degenerated elements, due to the combined effect of silencing pathways and elimination through deletions. One of the major difficulties in fully characterizing the molecular basis of genetic diversity of a given species lies in establishing its genome-wide transpositional activity. Here, we provide an extensive survey of the transpositional landscape of a plant genome using a deep sequencing strategy. This was achieved through paired-end mapping of a fourfold coverage of the genome of rice mutant line derived from an in vitro callus culture using Illumina technology. Our study shows that at least 13 TE families are active in this genotype, causing 34 new insertions. This next-generation sequencing-based strategy provides new opportunities to quantify the impact of TEs on the genome dynamics of the species., (© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.)
- Published
- 2011
- Full Text
- View/download PDF
9. Identification of an active LTR retrotransposon in rice.
- Author
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Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, and Panaud O
- Subjects
- DNA, Plant genetics, Gene Expression Profiling, Oligonucleotide Array Sequence Analysis, Phylogeny, Sequence Analysis, DNA, Genome, Plant, Oryza genetics, Retroelements, Terminal Repeat Sequences
- Abstract
Transposable elements are ubiquitous components of plant genomes. When active, these mobile elements can induce changes in the genome at both the structural and functional levels. Availability of the complete genome sequence for several model plant species provides the opportunity to study TEs in plants at an unprecedented scale. In the case of rice, annotation of the genomic sequence of the variety Nipponbare has revealed that TE-related sequences form more than 25% of its genome. However, most of the elements found are inactive, either because of structural alterations or because they are the target of various silencing pathways. In this paper, we propose a new post-genomic strategy aimed at identifying active TEs. Our approach relies on transcript profiling of TE-related sequences using a tiling microarray. We applied it to a particular class of TEs, the LTR retrotransposons. A transcript profiling assay of rice calli led to identification of a new transpositionally active family, named Lullaby. We provide a complete structural description of this element. We also show that it has recently been active in planta in rice, and discuss its phylogenetic relationships with Tos17, the only other active LTR retrotransposon described so far in the species.
- Published
- 2009
- Full Text
- View/download PDF
10. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.
- Author
-
Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, and Grigoriev IV
- Subjects
- Adaptation, Physiological, Chlorophyta classification, Chlorophyta cytology, Chlorophyta physiology, DNA Transposable Elements, Ecosystem, Gene Expression Regulation, Genes, Genetic Variation, Introns, Meiosis genetics, Molecular Sequence Data, Oceans and Seas, Photosynthesis genetics, Phylogeny, Phytoplankton classification, Phytoplankton genetics, RNA, Untranslated, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Transcription Factors genetics, Biological Evolution, Chlorophyta genetics, Genome, Plants genetics
- Abstract
Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
- Published
- 2009
- Full Text
- View/download PDF
11. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.
- Author
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Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, and Panaud O
- Subjects
- Computational Biology, Evolution, Molecular, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Phylogeny, Sequence Alignment, Gene Transfer, Horizontal, Oryza genetics, Retroelements, Sorghum genetics, Terminal Repeat Sequences, Zea mays genetics
- Abstract
Background: Horizontal transfers (HTs) refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs) in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum), as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae., Results: We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers., Conclusion: This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.
- Published
- 2009
- Full Text
- View/download PDF
12. Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza.
- Author
-
Roulin A, Piegu B, Wing RA, and Panaud O
- Subjects
- Base Sequence, Gene Expression Regulation, Plant genetics, Genes, Plant genetics, Phylogeny, Gene Transfer, Horizontal genetics, Oryza genetics, Plant Proteins genetics, Retroelements genetics, Terminal Repeat Sequences genetics
- Abstract
Horizontal gene transfer, defined as the transmission of genetic material between reproductively isolated species, has been considered for a long time to be a rare phenomenon. Most well-documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. Because of their propensity to increase their copy number while active, LTR retrotransposons can have a significant impact on genomics changes during evolution. In a previous study, we showed that in the wild rice species Oryza australiensis, 60% of the genome is composed of only three families of LTR retrotransposons named RIRE1, Wallabi and Kangourou. In the present study, using both in silico and experimental approaches, we show that one of these three families, RIRE1, has been transferred horizontally between O. australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants.
- Published
- 2008
- Full Text
- View/download PDF
13. The Rice Annotation Project Database (RAP-DB): 2008 update.
- Author
-
Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, and Echeverria M
- Subjects
- Genes, Plant, Genomics, Internet, MicroRNAs genetics, RNA, Small Interfering genetics, User-Computer Interface, Databases, Nucleic Acid, Genome, Plant, Oryza genetics
- Abstract
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
- Published
- 2008
- Full Text
- View/download PDF
14. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution.
- Author
-
Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, and Feuillet C
- Subjects
- Chromosomes, Plant genetics, Models, Genetic, Phylogeny, Sequence Alignment, Sequence Homology, Nucleic Acid, Species Specificity, Evolution, Molecular, Gene Duplication, Genome, Plant genetics, Oryza genetics, Triticum genetics
- Abstract
The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
- Published
- 2008
- Full Text
- View/download PDF
15. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza.
- Author
-
Ammiraju JS, 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, and Wing RA
- Subjects
- Genes, Plant, Phylogeny, Plant Proteins, Terminal Repeat Sequences, Evolution, Molecular, Genome, Plant, Multigene Family genetics, Oryza genetics, Retroelements genetics
- 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.
- Published
- 2007
- Full Text
- View/download PDF
16. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.
- Author
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Piegu B, Guyot R, Picault N, Roulin A, Sanyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, and Panaud O
- Subjects
- Base Sequence, Blotting, Southern, Chromosomes, Artificial, Bacterial, Cluster Analysis, Molecular Sequence Data, Sequence Analysis, DNA, Chromosome Mapping, Gene Duplication, Genome, Plant genetics, Oryza genetics, Phylogeny, Retroelements genetics
- Abstract
Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a "copy and paste" mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.
- Published
- 2006
- Full Text
- View/download PDF
17. An EST resource for cassava and other species of Euphorbiaceae.
- Author
-
Anderson JV, Delseny M, Fregene MA, Jorge V, Mba C, Lopez C, Restrepo S, Soto M, Piegu B, Verdier V, Cooke R, Tohme J, and Horvath DP
- Subjects
- Alleles, Chromosome Mapping, Euphorbiaceae classification, Gene Expression Profiling, Gene Frequency, Gene Library, Genes, Plant genetics, Genomics methods, Oligonucleotide Array Sequence Analysis, Plant Leaves genetics, Plant Roots genetics, Species Specificity, Euphorbiaceae genetics, Expressed Sequence Tags, Manihot genetics
- Abstract
Cassava (Manihot esculenta) is a major food staple for nearly 600 million people in Africa, Asia, and Latin America. Major losses in yield result from biotic and abiotic stresses that include diseases such as Cassava Mosaic Disease (CMD) and Cassava Bacterial Blight (CBB), drought, and acid soils. Additional losses also occur from deterioration during the post-harvest storage of roots. To help cassava breeders overcome these obstacles, the scientific community has turned to modern genomics approaches to identify key genetic characteristics associated with resistance to these yield-limiting factors. One approach for developing a genomics program requires the development of ESTs (expressed sequence tags). To date, nearly 23,000 ESTs have been developed from various cassava tissues, and genotypes. Preliminary analysis indicates existing EST resources contain at least 6000-7000 unigenes. Data presented in this report indicate that the cassava ESTs will be a valuable resource for the study of genetic diversity, stress resistance, and growth and development, not only in cassava, but also other members of the Euphorbiaceae family.
- Published
- 2004
- Full Text
- View/download PDF
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