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Biblioteca (s) : |
INIA Treinta y Tres. |
Fecha : |
21/02/2014 |
Actualizado : |
13/09/2018 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Autor : |
NOYES, N.R.; WEINROTH, M.E.; PARKER, J.K.; DEAN, C.J.; LAKIN, S.M.; RAYMOND, R.A.; ROVIRA, P.J.; DOSTER, E.; ABDO, Z.; MARTIN, J.N.; JONES, K.L.; RUIZ, J.; BOUCHER, C.A.; BELK, K.E.; MORLEY, P.S. |
Afiliación : |
NOELLE R. NOYES; MAGGIE E. WEINROTH; JENNIFER K. PARKER; CHRIS J. DEAN; STEVEN M. LAKIN; ROBERT A. RAYMOND; PABLO JUAN ROVIRA SANZ, INIA (Instituto Nacional de Investigación Agropecuaria), Uruguay; ENRIQUE DOSTER; ZAID ABDO; JENNIFER N. MARTIN; KENNETH L. JONES; JAIME RUIZ; CHRISTINA A. BOUCHER; KEITH E. BELK; PAUL S. MORLEY. |
Título : |
Enrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing. |
Fecha de publicación : |
2017 |
Fuente / Imprenta : |
Microbiome, 2017, 5, p. 142 |
Páginas : |
13 p. |
DOI : |
10.1186/s40168-017-0361-8 |
Idioma : |
Inglés |
Notas : |
Article History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 |
Contenido : |
Background: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins.
Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of
microbiome-resistome dynamics. MenosBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias.
Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional
metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistan... Presentar Todo |
Palabras claves : |
ANTIMICROBIAL RESISTANCE; METAGENÓMICA; MICROBIAL ECOLOGY; MOLECULAR ENRICHMENT; RARE MICROBIOME; RESISTOME. |
Thesagro : |
ANALISIS BIOLOGICO; ECOLOGIA MICROBIANA; RESISTENCIA A AGENTES DANINOS. |
Asunto categoría : |
U30 Métodos de investigación |
Marc : |
LEADER 03225naa a2200433 a 4500 001 1032862 005 2018-09-13 008 2017 bl uuuu u00u1 u #d 024 7 $a10.1186/s40168-017-0361-8$2DOI 100 1 $aNOYES, N.R. 245 $aEnrichment allows identification of diverse, rate elements in metagenomic resistome-virulome sequencing.$h[electronic resource] 260 $c2017 300 $a13 p. 500 $aArticle History: Received: 29 May 2017, Accepted: 5 October 2017, Published: 17 October 2017 520 $aBackground: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to imitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. Results: The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. Conclusions: These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistomevirulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics. 650 $aANALISIS BIOLOGICO 650 $aECOLOGIA MICROBIANA 650 $aRESISTENCIA A AGENTES DANINOS 653 $aANTIMICROBIAL RESISTANCE 653 $aMETAGENÓMICA 653 $aMICROBIAL ECOLOGY 653 $aMOLECULAR ENRICHMENT 653 $aRARE MICROBIOME 653 $aRESISTOME 700 1 $aWEINROTH, M.E. 700 1 $aPARKER, J.K. 700 1 $aDEAN, C.J. 700 1 $aLAKIN, S.M. 700 1 $aRAYMOND, R.A. 700 1 $aROVIRA, P.J. 700 1 $aDOSTER, E. 700 1 $aABDO, Z. 700 1 $aMARTIN, J.N. 700 1 $aJONES, K.L. 700 1 $aRUIZ, J. 700 1 $aBOUCHER, C.A. 700 1 $aBELK, K.E. 700 1 $aMORLEY, P.S. 773 $tMicrobiome, 2017, 5, p. 142
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Biblioteca (s) : |
INIA Las Brujas. |
Fecha actual : |
25/02/2021 |
Actualizado : |
25/02/2021 |
Tipo de producción científica : |
Artículos en Revistas Indexadas Internacionales |
Circulación / Nivel : |
Internacional - -- |
Autor : |
MILECH, C. G.; DINI, M.; SCARIOTTO, S.; SANTOS, J.; HERTER, F. G.; RASEIRA, M. C. B. |
Afiliación : |
C. G. MILECH, Postgraduate Program in Agronomy (PPGA), Faculty of Agronomy 'Eliseu Maciel', Federal University of Pelotas (FAEM-UFPel), Pelotas/RS, Brazil; MAXIMILIANO ANTONIO DINI VIÑOLY, Postgraduate Program in Agronomy (PPGA), Faculty of Agronomy 'Eliseu Maciel', Federal University of Pelotas (FAEM-UFPel), Pelotas/RS, Brazil; S. SCARIOTTO, Laboratory of Fruit Breeding, Embrapa Clima Temperado, Pelotas/RS, Brazil; J. SANTOS, Federal University of Maranhao (UFMA), Sao Luís/MA, Brazil; F. G. HERTER, Postgraduate Program in Agronomy (PPGA), Faculty of Agronomy 'Eliseu Maciel', Federal University of Pelotas (FAEM-UFPel), Pelotas/RS, Brazil; M. C. B. RASEIRA, Laboratory of Fruit Breeding, Embrapa Clima Temperado, Pelotas/RS, Brazil. |
Título : |
Chilling requirement of ten peach cultivars estimated by different models. |
Complemento del título : |
Original Research Article. |
Fecha de publicación : |
2018 |
Fuente / Imprenta : |
Journal of Experimental Agriculture International, February 2018, Volume 20, Issue 4, p. 1-9. Article no.JEAI.39204. DOI: https://doi.org/10.9734/JEAI/2018/39204 |
ISSN : |
2457-0591 |
DOI : |
10.9734/JEAI/2018/39204 |
Idioma : |
Inglés |
Notas : |
Article history: Received 23 November 2017; Accepted 31 January 2018; Published 8 February 2018.
Authors' contributions: This work was carried out in collaboration between all authors.Authors CGM, FGHand MCBR designed the study, wrote the protocol and wrote the first draft of the manuscript. Authors MD, SS and JS performed the statistical analysis and managed the literature searches. Author MCBR managed the analyses of the study. All authors read and approved the final manuscript. |
Contenido : |
ABSTRACT.
The adaptation of a temperate climate fruit cultivar to a certain area depends mainly on its chilling requirement and the chilling accumulation in such places. Several attempts have been made to estimate these two conditions, using different models. The great variation among the models to calculate chilling requirement makes it necessary to determine their efficiency in a given location. Aiming to estimate the chilling requirement of ten peach cultivars, including Bonão, Pepita, Maravilha, Precocinho, Turmalina, Diamante, BR-3, Marfim, Coral, and Cambará do Sul, seven models were tested: Utah, Positive Utah, Low Chill, Taiwan, Chilling Hours (≤7.2°C), Chilling Hours (≤11°C), and Dynamic. The results showed that the estimation of chilling accumulation for all the studied cultivars in all the tested models showed a large variability. None of the tested models was perfect for estimating the chilling requirement, especially considering the variable climatic conditions of southern Brazil. Except for the Utah model, any of the others can be used to provide a rough estimate of the chilling requirement of the cultivars; however, the Taiwan and Low Chill models seem to be more suitable. The chilling requirement, which was estimated based on the average over the 11 years of the study, overestimated the real need, when compared to the yields over those years. There are differences among the studied cultivars; however, with the exception of Cambará do Sul, all the others can yield good crops and show good adaptation to the climatic conditions of the southern Rio Grande do Sul.
© Copyright 2010-Till Date, Journal of Experimental Agriculture International. All rights reserved. MenosABSTRACT.
The adaptation of a temperate climate fruit cultivar to a certain area depends mainly on its chilling requirement and the chilling accumulation in such places. Several attempts have been made to estimate these two conditions, using different models. The great variation among the models to calculate chilling requirement makes it necessary to determine their efficiency in a given location. Aiming to estimate the chilling requirement of ten peach cultivars, including Bonão, Pepita, Maravilha, Precocinho, Turmalina, Diamante, BR-3, Marfim, Coral, and Cambará do Sul, seven models were tested: Utah, Positive Utah, Low Chill, Taiwan, Chilling Hours (≤7.2°C), Chilling Hours (≤11°C), and Dynamic. The results showed that the estimation of chilling accumulation for all the studied cultivars in all the tested models showed a large variability. None of the tested models was perfect for estimating the chilling requirement, especially considering the variable climatic conditions of southern Brazil. Except for the Utah model, any of the others can be used to provide a rough estimate of the chilling requirement of the cultivars; however, the Taiwan and Low Chill models seem to be more suitable. The chilling requirement, which was estimated based on the average over the 11 years of the study, overestimated the real need, when compared to the yields over those years. There are differences among the studied cultivars; however, with the exception of Cambará do Sul, all the ... Presentar Todo |
Palabras claves : |
Adaptation; Chill hours; Chill portions; Chill units; DORMANCY. |
Thesagro : |
PRUNUS PERSICA. |
Asunto categoría : |
F30 Genética vegetal y fitomejoramiento |
URL : |
http://www.ainfo.inia.uy/digital/bitstream/item/15101/1/984-Article-Text-1737-1-10-20181009.pdf
https://www.journaljeai.com/index.php/JEAI/article/download/984/1375/
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Marc : |
LEADER 03090naa a2200289 a 4500 001 1061768 005 2021-02-25 008 2018 bl uuuu u00u1 u #d 022 $a2457-0591 024 7 $a10.9734/JEAI/2018/39204$2DOI 100 1 $aMILECH, C. G. 245 $aChilling requirement of ten peach cultivars estimated by different models.$h[electronic resource] 260 $c2018 500 $aArticle history: Received 23 November 2017; Accepted 31 January 2018; Published 8 February 2018. Authors' contributions: This work was carried out in collaboration between all authors.Authors CGM, FGHand MCBR designed the study, wrote the protocol and wrote the first draft of the manuscript. Authors MD, SS and JS performed the statistical analysis and managed the literature searches. Author MCBR managed the analyses of the study. All authors read and approved the final manuscript. 520 $aABSTRACT. The adaptation of a temperate climate fruit cultivar to a certain area depends mainly on its chilling requirement and the chilling accumulation in such places. Several attempts have been made to estimate these two conditions, using different models. The great variation among the models to calculate chilling requirement makes it necessary to determine their efficiency in a given location. Aiming to estimate the chilling requirement of ten peach cultivars, including Bonão, Pepita, Maravilha, Precocinho, Turmalina, Diamante, BR-3, Marfim, Coral, and Cambará do Sul, seven models were tested: Utah, Positive Utah, Low Chill, Taiwan, Chilling Hours (≤7.2°C), Chilling Hours (≤11°C), and Dynamic. The results showed that the estimation of chilling accumulation for all the studied cultivars in all the tested models showed a large variability. None of the tested models was perfect for estimating the chilling requirement, especially considering the variable climatic conditions of southern Brazil. Except for the Utah model, any of the others can be used to provide a rough estimate of the chilling requirement of the cultivars; however, the Taiwan and Low Chill models seem to be more suitable. The chilling requirement, which was estimated based on the average over the 11 years of the study, overestimated the real need, when compared to the yields over those years. There are differences among the studied cultivars; however, with the exception of Cambará do Sul, all the others can yield good crops and show good adaptation to the climatic conditions of the southern Rio Grande do Sul. © Copyright 2010-Till Date, Journal of Experimental Agriculture International. All rights reserved. 650 $aPRUNUS PERSICA 653 $aAdaptation 653 $aChill hours 653 $aChill portions 653 $aChill units 653 $aDORMANCY 700 1 $aDINI, M. 700 1 $aSCARIOTTO, S. 700 1 $aSANTOS, J. 700 1 $aHERTER, F. G. 700 1 $aRASEIRA, M. C. B. 773 $tJournal of Experimental Agriculture International, February 2018, Volume 20, Issue 4, p. 1-9. Article no.JEAI.39204. DOI: https://doi.org/10.9734/JEAI/2018/39204
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