Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome

Vincentz, Michel; Cara, Frank A.A.; Okura, Vagner Katsumi; Silva, Felipe Rodrigues da; Pedrosa, Guilherme; Hemerly, Adriana S.; Capella, A.; Marins, Mozart; Ferreira, Paulo Sérgio; França, Suzelei C.; Grivet, Laurent; Vettore, André Luiz; Kemper, Edson L.; Burnquist, Willian L.; Targon, M. L. P. N.; Siqueira, Walter José; Kuramae, Eiko E.; Marino, Celso Luís; Camargo, L. E. A.; Carrer, Helaine; Coutinho, Luiz Lehmann; Furlan, Luiz Roberto; Lemos, Manoel Victor Franco; Nunes, Luiz R.; Gomes, Suely L.; Santelli, Roberto Vicente; Goldman, Maria Helena S.; Bacci, Maurício; Giglioti, Éder Antônio; Thiemann, Otávio Henrique; Silva, Flávio H.; Sluys, Marie‐Anne Van; Nóbrega, Francisco G.; Arruda, Paulo; Menck, Carlos Frederico Martins

doi:10.1104/pp.103.033878

Cited by 37 publications

(23 citation statements)

References 53 publications

(35 reference statements)

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“…Although 69% of the gene families in grasses is also present in eudicots, 3,006 gene families are unique to the grasses, of which 42% represent grass-specific families found in multiple cereals. These results correspond with previous estimates of putative monocotspecific genes using sugarcane (Saccharum officinarum) ESTs (Vincentz et al, 2004). In addition, we found that 11% of all families present in the grasses with homologs in eudicots were absent in Arabidopsis, which confirms our findings that gene loss in specific lineages or species is common.…”

Section: A Closer Look At Arabidopsis and Ricesupporting

confidence: 82%

“…In addition, we found that 11% of all families present in the grasses with homologs in eudicots were absent in Arabidopsis, which confirms our findings that gene loss in specific lineages or species is common. This number is considerably higher than the 2% of sugarcane sequences that matched homologous non-Arabidopsis eudicot sequences and is most probably caused by the higher number of eudicotyledonous species used here, compared with the analysis of Vincentz et al (2004). The reverse query indicates that also 11% of all families conserved between monocots and eudicots are absent in rice, suggesting that the amount species-specific gene loss in monocots and eudicots is very similar.…”

Section: A Closer Look At Arabidopsis and Ricementioning

confidence: 73%

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Exploring the Plant Transcriptome through Phylogenetic Profiling

Vandepoele

Peer

2005

Plant Physiology

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Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species-and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.

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Section: A Closer Look At Arabidopsis and Ricesupporting

confidence: 82%

Section: A Closer Look At Arabidopsis and Ricementioning

confidence: 73%

Exploring the Plant Transcriptome through Phylogenetic Profiling

Vandepoele

Peer

2005

Plant Physiology

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“…Tomato belongs to Solanaceae family (Vincentz et al, 2004) and was initially classified into the genus lycopersicon and the species esculentum. Based on molecular phylogenetic studies, tomato has been renamed Solanum lycopersicum (Peralta et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

2-deoxyglucose selection system for Agrobacterium-mediated transformation of Solanum lycopersicon and Nicotiana tabacum plants

et al. 2017

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An alternative marker to antibiotic and herbicide genes, 2-deoxyglucose-6-phosphate phosphatase (DOG R 1) gene was used to produce transgenic tomato (Solanum lycopersicon) and tobacco plants (Nicotiana tabacum) via Agrobacterium-mediated transformation approach. A binary vector, pBIDOG with T-DNA cassette consists of CaMV35S-DOG R 1-nos was mobilized into Agrobacterium tumefaciens LBA4404 via electroporation and subsequently transformed into tomato and tobacco tissues. Selection of transformants of both plants was carried out by using 600 mg/l 2-deoxyglucose (2-DOG) as selection agent. 2-DOG resistant calli were regenerated into shoots and PCR analysis revealed that 75% and 71% of putative transgenic tomato and tobacco shoots were positive for DOG R 1 gene, respectively. Southern blot analysis was carried out to confirm the integration of transgene. The expected ~1.5 kb band was obtained to prove the integration of DOG R 1 gene into the plant genome. Transgenic tomato and tobacco plants were successfully regenerated without any phenotypic changes when compared to wild-type plants. Therefore, this alternative selection system can be applied to other plant transformation systems to produce transgenic plants free from antibiotic and herbicide genes, especially for important economic crops. More importantly, this selection system does not lead to any extent hazard to human and animal that subsequently will improve public acceptance of future genetically modified products.

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“…Os desvios da colinearidade e sintenia se devem a diversos fatores, como duplicações e segmentações cromossômicas, mobilidade de TEs, deleções de genes e rearranjos localizados (Paterson et al 2000). e seqüências que não mostraram homologia com nenhuma outra espécie analisada (13.5%), podendo representar novidades evolutivas ou seqüências de evolução muito rápida (Vincentz et al 2004).…”

Section: Genômica Comparativaunclassified

O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz

Junior¹,

Luiz²

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IV são, na verdade, transposases domesticadas. Foram completamente seqüenciados dois clones de BAC de cana-de-açúcar, um proveniente de cada parental do híbrido (Saccharum officinarum e Saccharum spontaneum), ambos contendo elementos da Classe III. Estes elementos foram caracterizados e a seqüência genômica de cana foi comparada com sua ortóloga em arroz, revelando um acúmulo de TEs nas regiões intergênicas. AbstractTransposable elements (TEs) constitute great part of eukaryote genetic material, in grasses, they comprise between 50-80% of the genome. Genome projects have significantly increased the amount of information about these elements, revealing their importance and allowing the development of new approaches for their study. The Mutator system (Mu) of maize is the most active and mutagenic plant transposon. Beyond the autonomous element, MuDR, the system comprises a very heterogeneous, in sequence and structure, set of elements, called (Feschotte et al. 2002). Apesar da origem e do papel biológico dessas seqüências móveis permanecerem desconhecidos, acredita-se que elas geram variabilidade genética e que, portanto, possuem grande importância para a plasticidade do genoma necessária à evolução (Flavell et al. 1997, Evgen´ev 2007. O efeito deletério da transposição pode ser minimizado pela manutenção de elementos em estado quiescente durante o crescimento e desenvolvimento normais da planta hospedeira. Por outro lado, a ativação desses elementos em situações de estresse aumentaria a taxa de mutação, possibilitando uma reestruturação do genoma, eventualmente aproveitada pela seleção natural de forma a melhorar a adaptação do organismo (McClintock 1956 e 1984, Wessler 1996 Os retroelementos estão divididos em dois grupos: retroelementos com LTRs (Longas Terminações Repetidas, na mesma direção) e retroelementos sem LTRs (Fig.1). O grupo com LTRs é composto de retrovírus e retrotransposons, que possuem uma organização similar. A diferença reside no fato dos retrotransposons não apresentarem, diferentemente dos retrovírus, o domínio env, que codifica uma glicoproteína capaz de formar o envelope protéico da partícula viral, conferindo assim o caráter infeccioso (Fosket 1994, Schmidt 1999. Os retrotransposons podem ainda ser separados em dois grupos, Ty1/copia e Ty3/gypsy (segundo a nomenclatura original de levedura e Drosophila), de acordo com a posição dos domínios protéicos INT e RTRNAseH dentro da poliproteína pol. Os retroelementos sem LTR se dividem em LINEs ("Long Interspersed Nuclear Elements") e SINEs ("Short Interspersed Nuclear Elements") ( Fig. 1). Os LINEs são elementos autônomos que codificam todas as enzimas necessárias para sua transposição, enquanto os SINEs, contendo apenas poucas centenas de pares de bases, são elementos defectivos que necessitam das enzimas em trans para completar seu ciclo replicativo (Smyth 1993, Schmidt 1999. Existem evidências que indicam que os SINEs parasitam a maquinaria de transposição dos LINEs (Ogiwara et al. 1999).Os transposons de plantas têm repetições terminais i...

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Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome

Cited by 37 publications

References 53 publications

Exploring the Plant Transcriptome through Phylogenetic Profiling

Exploring the Plant Transcriptome through Phylogenetic Profiling

2-deoxyglucose selection system for Agrobacterium-mediated transformation of Solanum lycopersicon and Nicotiana tabacum plants

O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz

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