Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

<p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Kudrna David [verfasserIn] Ammiraju Jetty SS [verfasserIn] Song Xiang [verfasserIn] Grattapaglia Dario [verfasserIn] Fonseca Paulo GS [verfasserIn] Brommonschenkel Sérgio [verfasserIn] San-Clemente Hélène [verfasserIn] Santos Mauro D [verfasserIn] Vautrin Sonia [verfasserIn] Prat Elisa [verfasserIn] Paiva Jorge AP [verfasserIn] Wing Rod A [verfasserIn] Freitas Ana T [verfasserIn] Bergès Hélène [verfasserIn] Grima-Pettenati Jacqueline [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 12(2011), 1, p 137
Übergeordnetes Werk:	volume:12 ; year:2011 ; number:1, p 137

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-12-137

Katalog-ID:	DOAJ06699831X

Internformat


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allfields	10.1186/1471-2164-12-137 doi (DE-627)DOAJ06699831X (DE-599)DOAJ075ea123f8f64394bd0604d0f445b69e DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Kudrna David verfasserin aut Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Biotechnology Genetics Ammiraju Jetty SS verfasserin aut Song Xiang verfasserin aut Grattapaglia Dario verfasserin aut Fonseca Paulo GS verfasserin aut Brommonschenkel Sérgio verfasserin aut San-Clemente Hélène verfasserin aut Santos Mauro D verfasserin aut Vautrin Sonia verfasserin aut Prat Elisa verfasserin aut Paiva Jorge AP verfasserin aut Wing Rod A verfasserin aut Freitas Ana T verfasserin aut Bergès Hélène verfasserin aut Grima-Pettenati Jacqueline verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 137 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 137 https://doi.org/10.1186/1471-2164-12-137 kostenfrei https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e kostenfrei http://www.biomedcentral.com/1471-2164/12/137 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 137
spelling	10.1186/1471-2164-12-137 doi (DE-627)DOAJ06699831X (DE-599)DOAJ075ea123f8f64394bd0604d0f445b69e DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Kudrna David verfasserin aut Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Biotechnology Genetics Ammiraju Jetty SS verfasserin aut Song Xiang verfasserin aut Grattapaglia Dario verfasserin aut Fonseca Paulo GS verfasserin aut Brommonschenkel Sérgio verfasserin aut San-Clemente Hélène verfasserin aut Santos Mauro D verfasserin aut Vautrin Sonia verfasserin aut Prat Elisa verfasserin aut Paiva Jorge AP verfasserin aut Wing Rod A verfasserin aut Freitas Ana T verfasserin aut Bergès Hélène verfasserin aut Grima-Pettenati Jacqueline verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 137 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 137 https://doi.org/10.1186/1471-2164-12-137 kostenfrei https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e kostenfrei http://www.biomedcentral.com/1471-2164/12/137 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 137
allfields_unstemmed	10.1186/1471-2164-12-137 doi (DE-627)DOAJ06699831X (DE-599)DOAJ075ea123f8f64394bd0604d0f445b69e DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Kudrna David verfasserin aut Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Biotechnology Genetics Ammiraju Jetty SS verfasserin aut Song Xiang verfasserin aut Grattapaglia Dario verfasserin aut Fonseca Paulo GS verfasserin aut Brommonschenkel Sérgio verfasserin aut San-Clemente Hélène verfasserin aut Santos Mauro D verfasserin aut Vautrin Sonia verfasserin aut Prat Elisa verfasserin aut Paiva Jorge AP verfasserin aut Wing Rod A verfasserin aut Freitas Ana T verfasserin aut Bergès Hélène verfasserin aut Grima-Pettenati Jacqueline verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 137 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 137 https://doi.org/10.1186/1471-2164-12-137 kostenfrei https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e kostenfrei http://www.biomedcentral.com/1471-2164/12/137 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 137
allfieldsGer	10.1186/1471-2164-12-137 doi (DE-627)DOAJ06699831X (DE-599)DOAJ075ea123f8f64394bd0604d0f445b69e DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Kudrna David verfasserin aut Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Biotechnology Genetics Ammiraju Jetty SS verfasserin aut Song Xiang verfasserin aut Grattapaglia Dario verfasserin aut Fonseca Paulo GS verfasserin aut Brommonschenkel Sérgio verfasserin aut San-Clemente Hélène verfasserin aut Santos Mauro D verfasserin aut Vautrin Sonia verfasserin aut Prat Elisa verfasserin aut Paiva Jorge AP verfasserin aut Wing Rod A verfasserin aut Freitas Ana T verfasserin aut Bergès Hélène verfasserin aut Grima-Pettenati Jacqueline verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 137 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 137 https://doi.org/10.1186/1471-2164-12-137 kostenfrei https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e kostenfrei http://www.biomedcentral.com/1471-2164/12/137 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 137
allfieldsSound	10.1186/1471-2164-12-137 doi (DE-627)DOAJ06699831X (DE-599)DOAJ075ea123f8f64394bd0604d0f445b69e DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Kudrna David verfasserin aut Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p< Biotechnology Genetics Ammiraju Jetty SS verfasserin aut Song Xiang verfasserin aut Grattapaglia Dario verfasserin aut Fonseca Paulo GS verfasserin aut Brommonschenkel Sérgio verfasserin aut San-Clemente Hélène verfasserin aut Santos Mauro D verfasserin aut Vautrin Sonia verfasserin aut Prat Elisa verfasserin aut Paiva Jorge AP verfasserin aut Wing Rod A verfasserin aut Freitas Ana T verfasserin aut Bergès Hélène verfasserin aut Grima-Pettenati Jacqueline verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 137 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 137 https://doi.org/10.1186/1471-2164-12-137 kostenfrei https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e kostenfrei http://www.biomedcentral.com/1471-2164/12/137 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 12 2011 1, p 137
language	English
source	In BMC Genomics 12(2011), 1, p 137 volume:12 year:2011 number:1, p 137
sourceStr	In BMC Genomics 12(2011), 1, p 137 volume:12 year:2011 number:1, p 137
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Kudrna David @@aut@@ Ammiraju Jetty SS @@aut@@ Song Xiang @@aut@@ Grattapaglia Dario @@aut@@ Fonseca Paulo GS @@aut@@ Brommonschenkel Sérgio @@aut@@ San-Clemente Hélène @@aut@@ Santos Mauro D @@aut@@ Vautrin Sonia @@aut@@ Prat Elisa @@aut@@ Paiva Jorge AP @@aut@@ Wing Rod A @@aut@@ Freitas Ana T @@aut@@ Bergès Hélène @@aut@@ Grima-Pettenati Jacqueline @@aut@@
publishDateDaySort_date	2011-01-01T00:00:00Z
hierarchy_top_id	326644954
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The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. 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callnumber-first	T - Technology
author	Kudrna David
spellingShingle	Kudrna David misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
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topic_title	TP248.13-248.65 QH426-470 Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
topic	misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics
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title	Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
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title_full	Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
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author_browse	Kudrna David Ammiraju Jetty SS Song Xiang Grattapaglia Dario Fonseca Paulo GS Brommonschenkel Sérgio San-Clemente Hélène Santos Mauro D Vautrin Sonia Prat Elisa Paiva Jorge AP Wing Rod A Freitas Ana T Bergès Hélène Grima-Pettenati Jacqueline
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title_sort	advancing <it<eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage bac libraries
callnumber	TP248.13-248.65
title_auth	Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
abstract	<p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<<it<Eucalyptus </it<species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p< <p<Results</p< <p<We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it<E. grandis </it<(clone BRASUZ1) digested with <it<Hind</it<III and <it<BstY</it<I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it<via </it<hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it<E. grandis </it<chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p< <p<Conclusions</p< <p<The two <it<E. grandis </it<BAC libraries described in this study represent an important milestone for the advancement of <it<Eucalyptus </it<genomics and forest tree research. These BAC resources have a highly redundant genome coverage (< 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it<Eucalyptus </it<and possibly in related species of <it<Myrtaceae</it<, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it<E. grandis </it<BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it<Eucalyptus </it<reference genome sequence.</p<
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container_issue	1, p 137
title_short	Advancing <it<Eucalyptus </it<genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
url	https://doi.org/10.1186/1471-2164-12-137 https://doaj.org/article/075ea123f8f64394bd0604d0f445b69e http://www.biomedcentral.com/1471-2164/12/137 https://doaj.org/toc/1471-2164
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author2Str	Ammiraju Jetty SS Song Xiang Grattapaglia Dario Fonseca Paulo GS Brommonschenkel Sérgio San-Clemente Hélène Santos Mauro D Vautrin Sonia Prat Elisa Paiva Jorge AP Wing Rod A Freitas Ana T Bergès Hélène Grima-Pettenati Jacqueline
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doi_str	10.1186/1471-2164-12-137
callnumber-a	TP248.13-248.65
up_date	2024-07-03T23:04:05.438Z
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