Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Le Provost Grégoire [verfasserIn] Bodénès Catherine [verfasserIn] Martin-Magniette Marie-Laure [verfasserIn] Bitton Frédérique [verfasserIn] Boussardon Clément [verfasserIn] Lesur Isabelle [verfasserIn] Faivre Rampant Patricia [verfasserIn] Bergès Hélène [verfasserIn] Fluch Sylvia [verfasserIn] Kremer Antoine [verfasserIn] Plomion Christophe [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2011

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 12(2011), 1, p 292
Übergeordnetes Werk:	volume:12 ; year:2011 ; number:1, p 292

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-12-292

Katalog-ID:	DOAJ06336073X

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allfields	10.1186/1471-2164-12-292 doi (DE-627)DOAJ06336073X (DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Le Provost Grégoire verfasserin aut Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Biotechnology Genetics Bodénès Catherine verfasserin aut Martin-Magniette Marie-Laure verfasserin aut Bitton Frédérique verfasserin aut Boussardon Clément verfasserin aut Lesur Isabelle verfasserin aut Faivre Rampant Patricia verfasserin aut Bergès Hélène verfasserin aut Fluch Sylvia verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 292 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 292 https://doi.org/10.1186/1471-2164-12-292 kostenfrei https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 kostenfrei http://www.biomedcentral.com/1471-2164/12/292 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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 292
spelling	10.1186/1471-2164-12-292 doi (DE-627)DOAJ06336073X (DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Le Provost Grégoire verfasserin aut Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Biotechnology Genetics Bodénès Catherine verfasserin aut Martin-Magniette Marie-Laure verfasserin aut Bitton Frédérique verfasserin aut Boussardon Clément verfasserin aut Lesur Isabelle verfasserin aut Faivre Rampant Patricia verfasserin aut Bergès Hélène verfasserin aut Fluch Sylvia verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 292 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 292 https://doi.org/10.1186/1471-2164-12-292 kostenfrei https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 kostenfrei http://www.biomedcentral.com/1471-2164/12/292 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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 292
allfields_unstemmed	10.1186/1471-2164-12-292 doi (DE-627)DOAJ06336073X (DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Le Provost Grégoire verfasserin aut Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Biotechnology Genetics Bodénès Catherine verfasserin aut Martin-Magniette Marie-Laure verfasserin aut Bitton Frédérique verfasserin aut Boussardon Clément verfasserin aut Lesur Isabelle verfasserin aut Faivre Rampant Patricia verfasserin aut Bergès Hélène verfasserin aut Fluch Sylvia verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 292 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 292 https://doi.org/10.1186/1471-2164-12-292 kostenfrei https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 kostenfrei http://www.biomedcentral.com/1471-2164/12/292 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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 292
allfieldsGer	10.1186/1471-2164-12-292 doi (DE-627)DOAJ06336073X (DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Le Provost Grégoire verfasserin aut Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Biotechnology Genetics Bodénès Catherine verfasserin aut Martin-Magniette Marie-Laure verfasserin aut Bitton Frédérique verfasserin aut Boussardon Clément verfasserin aut Lesur Isabelle verfasserin aut Faivre Rampant Patricia verfasserin aut Bergès Hélène verfasserin aut Fluch Sylvia verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 292 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 292 https://doi.org/10.1186/1471-2164-12-292 kostenfrei https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 kostenfrei http://www.biomedcentral.com/1471-2164/12/292 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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 292
allfieldsSound	10.1186/1471-2164-12-292 doi (DE-627)DOAJ06336073X (DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Le Provost Grégoire verfasserin aut Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome 2011 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p< Biotechnology Genetics Bodénès Catherine verfasserin aut Martin-Magniette Marie-Laure verfasserin aut Bitton Frédérique verfasserin aut Boussardon Clément verfasserin aut Lesur Isabelle verfasserin aut Faivre Rampant Patricia verfasserin aut Bergès Hélène verfasserin aut Fluch Sylvia verfasserin aut Kremer Antoine verfasserin aut Plomion Christophe verfasserin aut In BMC Genomics BMC, 2003 12(2011), 1, p 292 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:12 year:2011 number:1, p 292 https://doi.org/10.1186/1471-2164-12-292 kostenfrei https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 kostenfrei http://www.biomedcentral.com/1471-2164/12/292 kostenfrei https://doaj.org/toc/1471-2164 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ 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 292
language	English
source	In BMC Genomics 12(2011), 1, p 292 volume:12 year:2011 number:1, p 292
sourceStr	In BMC Genomics 12(2011), 1, p 292 volume:12 year:2011 number:1, p 292
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Le Provost Grégoire @@aut@@ Bodénès Catherine @@aut@@ Martin-Magniette Marie-Laure @@aut@@ Bitton Frédérique @@aut@@ Boussardon Clément @@aut@@ Lesur Isabelle @@aut@@ Faivre Rampant Patricia @@aut@@ Bergès Hélène @@aut@@ Fluch Sylvia @@aut@@ Kremer Antoine @@aut@@ Plomion Christophe @@aut@@
publishDateDaySort_date	2011-01-01T00:00:00Z
hierarchy_top_id	326644954
id	DOAJ06336073X
language_de	englisch
fullrecord	<?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01000caa a22002652 4500</leader><controlfield tag="001">DOAJ06336073X</controlfield><controlfield tag="003">DE-627</controlfield><controlfield tag="005">20230309030352.0</controlfield><controlfield tag="007">cr uuu---uuuuu</controlfield><controlfield tag="008">230228s2011 xx \|\|\|\|\|o 00\| \|\|eng c</controlfield><datafield tag="024" ind1="7" ind2=" "><subfield code="a">10.1186/1471-2164-12-292</subfield><subfield code="2">doi</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-627)DOAJ06336073X</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DOAJ51d9ada73fd641e2b8a96edefe46fc27</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-627</subfield><subfield code="b">ger</subfield><subfield code="c">DE-627</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1=" " ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">TP248.13-248.65</subfield></datafield><datafield tag="050" ind1=" " ind2="0"><subfield code="a">QH426-470</subfield></datafield><datafield tag="100" ind1="0" ind2=" "><subfield code="a">Le Provost Grégoire</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2011</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="a">Text</subfield><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="a">Computermedien</subfield><subfield code="b">c</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="a">Online-Ressource</subfield><subfield code="b">cr</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="520" ind1=" " ind2=" "><subfield code="a"><p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. 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author	Le Provost Grégoire
spellingShingle	Le Provost Grégoire misc TP248.13-248.65 misc QH426-470 misc Biotechnology misc Genetics Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
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topic_title	TP248.13-248.65 QH426-470 Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
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title	Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
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title_full	Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
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author_browse	Le Provost Grégoire Bodénès Catherine Martin-Magniette Marie-Laure Bitton Frédérique Boussardon Clément Lesur Isabelle Faivre Rampant Patricia Bergès Hélène Fluch Sylvia Kremer Antoine Plomion Christophe
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title_sort	analysis of bac end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
callnumber	TP248.13-248.65
title_auth	Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
abstract	<p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p<
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title_short	Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome
url	https://doi.org/10.1186/1471-2164-12-292 https://doaj.org/article/51d9ada73fd641e2b8a96edefe46fc27 http://www.biomedcentral.com/1471-2164/12/292 https://doaj.org/toc/1471-2164
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This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it<Quercus robur</it<, its characterization and an analysis of BAC end sequences.</p< <p<Results</p< <p<The <it<Eco</it<RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it<ab initio </it<repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it<Arabidopsis thaliana</it<, <it<Vitis vinifera </it<and <it<Populus trichocarpa</it<. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it<V. vinifera.</it<</p< <p<Conclusions</p< <p<This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. 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Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

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