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 | Acesso ao texto completo restrito à biblioteca da Embrapa Recursos Genéticos e Biotecnologia. Para informações adicionais entre em contato com cenargen.biblioteca@embrapa.br. |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
19/02/2013 |
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Data da última atualização: |
06/03/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
PETROLI, C. D.; SANSALONI, C. P; CARLING, J.; STEANE, D. A.; VAILLANCOURT, R. E.; MYBURG, A. M.; SILVA JUNIOR, O. B. da; PAPPAS JUNIOR, G. J.; KILIAN, A.; GRATTAPAGLIA, D. |
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Afiliação: |
CESAR D. PETROLI, UnB; CAROLINA P. SANSALONI, UnB; JASON CARLING, Diversity Arrays Technology Pty Ltd., Yarralumla, Australia; DOROTHY A. STEANE, University of Tasmania, Hobart, Tasmania, Australia; RENE E. VAILLANCOURT, University of Tasmania, Hobart, Tasmania, Australia; ALEXANDER A. MYBURG, University of Pretoria, Pretoria, South Africa; ORZENIL BONFIM DA SILVA JUNIOR, CENARGEN; GEORGIOS JOANNIS PAPPAS JUNIOR, CENARGEN; ANDRZEJ KILIAN, Diversity Arrays Technology Pty Ltd., Yarralumla, Australia; DARIO GRATTAPAGLIA, CENARGEN. |
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Título: |
Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. |
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Ano de publicação: |
2012 |
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Fonte/Imprenta: |
PLoS ONE, v. 7, n. 9, set. 2012. |
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Idioma: |
Inglês |
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Conteúdo: |
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. MenosDiversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in pla... Mostrar Tudo |
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Palavras-Chave: |
Caracterização genómica; Dart genotyping; Genoma do Eucalipto; Microsatellite genotyping. |
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Thesagro: |
Genoma. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02933naa a2200289 a 4500
001 1949877
005 2023-03-06
008 2012 bl uuuu u00u1 u #d
100 1 $aPETROLI, C. D.
245 $aGenomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.$h[electronic resource]
260 $c2012
520 $aDiversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
650 $aGenoma
653 $aCaracterização genómica
653 $aDart genotyping
653 $aGenoma do Eucalipto
653 $aMicrosatellite genotyping
700 1 $aSANSALONI, C. P
700 1 $aCARLING, J.
700 1 $aSTEANE, D. A.
700 1 $aVAILLANCOURT, R. E.
700 1 $aMYBURG, A. M.
700 1 $aSILVA JUNIOR, O. B. da
700 1 $aPAPPAS JUNIOR, G. J.
700 1 $aKILIAN, A.
700 1 $aGRATTAPAGLIA, D.
773 $tPLoS ONE$gv. 7, n. 9, set. 2012.
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Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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Registro Completo
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Biblioteca(s): |
Embrapa Meio Ambiente. |
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Data corrente: |
02/08/2018 |
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Data da última atualização: |
01/11/2018 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
GENUÁRIO, D. B.; SOUZA, W. R.; MONTEIRO, R. T. R.; SANT'ANNA, C. L.; MELO, I. S. de. |
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Afiliação: |
DIEGO BONALDO GENUARIO, FAPESP; WALLACE RAFAEL DE SOUZA, CENA-USP; REGINA TERESA ROSIN MONTEIRO, CENA-USP; CELIA LEITE SANT'ANNA, IB São Paulo; ITAMAR SOARES DE MELO, CNPMA. |
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Título: |
Amazoninema gen. nov., (Synechococcales, Pseudanabaenaceae) a novel cyanobacteria genus from Brazilian Amazonian rivers. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
International Journal of Systematic and Evolutionary Microbiology, v. 68, n. 7, p. 2249-2257, 2018. |
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DOI: |
https://doi.org/10.1099/ijsem.0.00282 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract: The genus Leptolyngbya includes morphotypes with thin cells and simple morphology, and is one of the most common cyanobacterial genera found in a wide range of environments. In many cases, however, the morphotypes assigned to this genus do not share a common ancestor based on 16S rRNA gene phylogeny, which has led to the description of novel genera, such as Nodosilinea, Oculatella, Pantanalinema , Alkalinema , Thermoleptolyngbya, Onodrimia, Timaviella and Toxifilum. Thus, four novel isolates, with a comparable morphology to Leptolyngbya , were recovered from the Amazon and Solimões rivers. The novel 16S rRNA gene sequences obtained from these strains were placed together as a new and distinct phylogenetic lineage that is more closely related to the clusters embracing the genera Nodosilinea, Haloleptolyngbya and Halomicronema than to the genus Leptolyngbya . Additionally, these novel 16S rRNA gene sequences showed similarity values lower than 95% compared with those from the most phylogenetic related groups and/or established genera. Altogether, these results supported the erection of a novel genus, named Amazoninema, to accommodate the novel isolates. Likewise, a comparison of their 16S rRNA gene sequences revealed similarities higher than 99.8%, indicating that they belong to a single species, which was corroborated by analysing their 16S-23S internal transcribed spacer regions and unique Box-B helix pattern. Few studies have been undertaken to uncover the cultured diversity of cyanobacteria from Amazonia, and to our knowledge, this is the first cyanobacteria genus erected, considering morphotypes isolated exclusively from Brazilian Amazonian rivers. MenosAbstract: The genus Leptolyngbya includes morphotypes with thin cells and simple morphology, and is one of the most common cyanobacterial genera found in a wide range of environments. In many cases, however, the morphotypes assigned to this genus do not share a common ancestor based on 16S rRNA gene phylogeny, which has led to the description of novel genera, such as Nodosilinea, Oculatella, Pantanalinema , Alkalinema , Thermoleptolyngbya, Onodrimia, Timaviella and Toxifilum. Thus, four novel isolates, with a comparable morphology to Leptolyngbya , were recovered from the Amazon and Solimões rivers. The novel 16S rRNA gene sequences obtained from these strains were placed together as a new and distinct phylogenetic lineage that is more closely related to the clusters embracing the genera Nodosilinea, Haloleptolyngbya and Halomicronema than to the genus Leptolyngbya . Additionally, these novel 16S rRNA gene sequences showed similarity values lower than 95% compared with those from the most phylogenetic related groups and/or established genera. Altogether, these results supported the erection of a novel genus, named Amazoninema, to accommodate the novel isolates. Likewise, a comparison of their 16S rRNA gene sequences revealed similarities higher than 99.8%, indicating that they belong to a single species, which was corroborated by analysing their 16S-23S internal transcribed spacer regions and unique Box-B helix pattern. Few studies have been undertaken to uncover the culture... Mostrar Tudo |
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Palavras-Chave: |
16S rRNA gene; Cianobactéria; Halomicronema; ITS secondary structures; Nodosilinea. |
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Thesagro: |
Bactéria. |
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Thesaurus NAL: |
Amazon River; Brazil; Cyanobacteria; Leptolyngbya. |
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Categoria do assunto: |
V Taxonomia de Organismos |
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Marc: |
LEADER 02643naa a2200301 a 4500
001 2093821
005 2018-11-01
008 2018 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1099/ijsem.0.00282$2DOI
100 1 $aGENUÁRIO, D. B.
245 $aAmazoninema gen. nov., (Synechococcales, Pseudanabaenaceae) a novel cyanobacteria genus from Brazilian Amazonian rivers.$h[electronic resource]
260 $c2018
520 $aAbstract: The genus Leptolyngbya includes morphotypes with thin cells and simple morphology, and is one of the most common cyanobacterial genera found in a wide range of environments. In many cases, however, the morphotypes assigned to this genus do not share a common ancestor based on 16S rRNA gene phylogeny, which has led to the description of novel genera, such as Nodosilinea, Oculatella, Pantanalinema , Alkalinema , Thermoleptolyngbya, Onodrimia, Timaviella and Toxifilum. Thus, four novel isolates, with a comparable morphology to Leptolyngbya , were recovered from the Amazon and Solimões rivers. The novel 16S rRNA gene sequences obtained from these strains were placed together as a new and distinct phylogenetic lineage that is more closely related to the clusters embracing the genera Nodosilinea, Haloleptolyngbya and Halomicronema than to the genus Leptolyngbya . Additionally, these novel 16S rRNA gene sequences showed similarity values lower than 95% compared with those from the most phylogenetic related groups and/or established genera. Altogether, these results supported the erection of a novel genus, named Amazoninema, to accommodate the novel isolates. Likewise, a comparison of their 16S rRNA gene sequences revealed similarities higher than 99.8%, indicating that they belong to a single species, which was corroborated by analysing their 16S-23S internal transcribed spacer regions and unique Box-B helix pattern. Few studies have been undertaken to uncover the cultured diversity of cyanobacteria from Amazonia, and to our knowledge, this is the first cyanobacteria genus erected, considering morphotypes isolated exclusively from Brazilian Amazonian rivers.
650 $aAmazon River
650 $aBrazil
650 $aCyanobacteria
650 $aLeptolyngbya
650 $aBactéria
653 $a16S rRNA gene
653 $aCianobactéria
653 $aHalomicronema
653 $aITS secondary structures
653 $aNodosilinea
700 1 $aSOUZA, W. R.
700 1 $aMONTEIRO, R. T. R.
700 1 $aSANT'ANNA, C. L.
700 1 $aMELO, I. S. de
773 $tInternational Journal of Systematic and Evolutionary Microbiology$gv. 68, n. 7, p. 2249-2257, 2018.
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