<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs

<p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it&l...
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Gespeichert in:

Autor*in:	Hassan Musa A [verfasserIn] Melo Mariane B [verfasserIn] Haas Brian [verfasserIn] Jensen Kirk D C [verfasserIn] Saeij Jeroen P J [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	RNA-seq Trinity LincRNA Alternative splicing Transcriptome

Übergeordnetes Werk:	In: BMC Genomics - BMC, 2003, 13(2012), 1, p 696
Übergeordnetes Werk:	volume:13 ; year:2012 ; number:1, p 696

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/1471-2164-13-696

Katalog-ID:	DOAJ057754519

Internformat


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520			\|a <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p<
650		4	\|a <it<Toxoplasma</it<
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650		4	\|a Alternative splicing
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700	0		\|a Saeij Jeroen P J \|e verfasserin \|4 aut
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912			\|a GBV_ILN_22
912			\|a GBV_ILN_23
912			\|a GBV_ILN_24
912			\|a GBV_ILN_39
912			\|a GBV_ILN_40
912			\|a GBV_ILN_60
912			\|a GBV_ILN_62
912			\|a GBV_ILN_63
912			\|a GBV_ILN_65
912			\|a GBV_ILN_69
912			\|a GBV_ILN_70
912			\|a GBV_ILN_73
912			\|a GBV_ILN_74
912			\|a GBV_ILN_95
912			\|a GBV_ILN_105
912			\|a GBV_ILN_110
912			\|a GBV_ILN_151
912			\|a GBV_ILN_161
912			\|a GBV_ILN_170
912			\|a GBV_ILN_206
912			\|a GBV_ILN_213
912			\|a GBV_ILN_230
912			\|a GBV_ILN_285
912			\|a GBV_ILN_293
912			\|a GBV_ILN_602
912			\|a GBV_ILN_702
912			\|a GBV_ILN_2001
912			\|a GBV_ILN_2003
912			\|a GBV_ILN_2005
912			\|a GBV_ILN_2006
912			\|a GBV_ILN_2008
912			\|a GBV_ILN_2009
912			\|a GBV_ILN_2010
912			\|a GBV_ILN_2011
912			\|a GBV_ILN_2014
912			\|a GBV_ILN_2015
912			\|a GBV_ILN_2020
912			\|a GBV_ILN_2021
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912			\|a GBV_ILN_2031
912			\|a GBV_ILN_2038
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912			\|a GBV_ILN_2056
912			\|a GBV_ILN_2057
912			\|a GBV_ILN_2061
912			\|a GBV_ILN_2111
912			\|a GBV_ILN_2113
912			\|a GBV_ILN_2190
912			\|a GBV_ILN_4012
912			\|a GBV_ILN_4037
912			\|a GBV_ILN_4112
912			\|a GBV_ILN_4125
912			\|a GBV_ILN_4126
912			\|a GBV_ILN_4249
912			\|a GBV_ILN_4305
912			\|a GBV_ILN_4306
912			\|a GBV_ILN_4307
912			\|a GBV_ILN_4313
912			\|a GBV_ILN_4322
912			\|a GBV_ILN_4323
912			\|a GBV_ILN_4324
912			\|a GBV_ILN_4325
912			\|a GBV_ILN_4338
912			\|a GBV_ILN_4367
912			\|a GBV_ILN_4700
951			\|a AR
952			\|d 13 \|j 2012 \|e 1, p 696

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author_variant	h m a hma m m b mmb h b hb j k d c jkdc s j p j sjpj
matchkey_str	article:14712164:2012----::teooteosrcinfhitxpamgniitasrpoemrvsnhcreteoenoainnrvaslentvls
hierarchy_sort_str	2012
callnumber-subject-code	TP
publishDate	2012
allfields	10.1186/1471-2164-13-696 doi (DE-627)DOAJ057754519 (DE-599)DOAJae97bb3ab2fb41cf9ab086fb29254822 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Hassan Musa A verfasserin aut <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p< <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics Melo Mariane B verfasserin aut Haas Brian verfasserin aut Jensen Kirk D C verfasserin aut Saeij Jeroen P J verfasserin aut In BMC Genomics BMC, 2003 13(2012), 1, p 696 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:13 year:2012 number:1, p 696 https://doi.org/10.1186/1471-2164-13-696 kostenfrei https://doaj.org/article/ae97bb3ab2fb41cf9ab086fb29254822 kostenfrei http://www.biomedcentral.com/1471-2164/13/696 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 13 2012 1, p 696
spelling	10.1186/1471-2164-13-696 doi (DE-627)DOAJ057754519 (DE-599)DOAJae97bb3ab2fb41cf9ab086fb29254822 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Hassan Musa A verfasserin aut <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p< <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics Melo Mariane B verfasserin aut Haas Brian verfasserin aut Jensen Kirk D C verfasserin aut Saeij Jeroen P J verfasserin aut In BMC Genomics BMC, 2003 13(2012), 1, p 696 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:13 year:2012 number:1, p 696 https://doi.org/10.1186/1471-2164-13-696 kostenfrei https://doaj.org/article/ae97bb3ab2fb41cf9ab086fb29254822 kostenfrei http://www.biomedcentral.com/1471-2164/13/696 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 13 2012 1, p 696
allfields_unstemmed	10.1186/1471-2164-13-696 doi (DE-627)DOAJ057754519 (DE-599)DOAJae97bb3ab2fb41cf9ab086fb29254822 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Hassan Musa A verfasserin aut <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p< <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics Melo Mariane B verfasserin aut Haas Brian verfasserin aut Jensen Kirk D C verfasserin aut Saeij Jeroen P J verfasserin aut In BMC Genomics BMC, 2003 13(2012), 1, p 696 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:13 year:2012 number:1, p 696 https://doi.org/10.1186/1471-2164-13-696 kostenfrei https://doaj.org/article/ae97bb3ab2fb41cf9ab086fb29254822 kostenfrei http://www.biomedcentral.com/1471-2164/13/696 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 13 2012 1, p 696
allfieldsGer	10.1186/1471-2164-13-696 doi (DE-627)DOAJ057754519 (DE-599)DOAJae97bb3ab2fb41cf9ab086fb29254822 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Hassan Musa A verfasserin aut <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p< <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics Melo Mariane B verfasserin aut Haas Brian verfasserin aut Jensen Kirk D C verfasserin aut Saeij Jeroen P J verfasserin aut In BMC Genomics BMC, 2003 13(2012), 1, p 696 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:13 year:2012 number:1, p 696 https://doi.org/10.1186/1471-2164-13-696 kostenfrei https://doaj.org/article/ae97bb3ab2fb41cf9ab086fb29254822 kostenfrei http://www.biomedcentral.com/1471-2164/13/696 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 13 2012 1, p 696
allfieldsSound	10.1186/1471-2164-13-696 doi (DE-627)DOAJ057754519 (DE-599)DOAJae97bb3ab2fb41cf9ab086fb29254822 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QH426-470 Hassan Musa A verfasserin aut <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p< <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics Melo Mariane B verfasserin aut Haas Brian verfasserin aut Jensen Kirk D C verfasserin aut Saeij Jeroen P J verfasserin aut In BMC Genomics BMC, 2003 13(2012), 1, p 696 (DE-627)326644954 (DE-600)2041499-7 14712164 nnns volume:13 year:2012 number:1, p 696 https://doi.org/10.1186/1471-2164-13-696 kostenfrei https://doaj.org/article/ae97bb3ab2fb41cf9ab086fb29254822 kostenfrei http://www.biomedcentral.com/1471-2164/13/696 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 13 2012 1, p 696
language	English
source	In BMC Genomics 13(2012), 1, p 696 volume:13 year:2012 number:1, p 696
sourceStr	In BMC Genomics 13(2012), 1, p 696 volume:13 year:2012 number:1, p 696
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	<it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome Biotechnology Genetics
isfreeaccess_bool	true
container_title	BMC Genomics
authorswithroles_txt_mv	Hassan Musa A @@aut@@ Melo Mariane B @@aut@@ Haas Brian @@aut@@ Jensen Kirk D C @@aut@@ Saeij Jeroen P J @@aut@@
publishDateDaySort_date	2012-01-01T00:00:00Z
hierarchy_top_id	326644954
id	DOAJ057754519
language_de	englisch
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callnumber-first	T - Technology
author	Hassan Musa A
spellingShingle	Hassan Musa A misc TP248.13-248.65 misc QH426-470 misc <it<Toxoplasma</it< misc RNA-seq misc Trinity misc LincRNA misc Alternative splicing misc Transcriptome misc Biotechnology misc Genetics <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
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topic_title	TP248.13-248.65 QH426-470 <it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs <it<Toxoplasma</it< RNA-seq Trinity LincRNA Alternative splicing Transcriptome
topic	misc TP248.13-248.65 misc QH426-470 misc <it<Toxoplasma</it< misc RNA-seq misc Trinity misc LincRNA misc Alternative splicing misc Transcriptome misc Biotechnology misc Genetics
topic_unstemmed	misc TP248.13-248.65 misc QH426-470 misc <it<Toxoplasma</it< misc RNA-seq misc Trinity misc LincRNA misc Alternative splicing misc Transcriptome misc Biotechnology misc Genetics
topic_browse	misc TP248.13-248.65 misc QH426-470 misc <it<Toxoplasma</it< misc RNA-seq misc Trinity misc LincRNA misc Alternative splicing misc Transcriptome misc Biotechnology misc Genetics
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title	<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
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title_full	<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
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author_browse	Hassan Musa A Melo Mariane B Haas Brian Jensen Kirk D C Saeij Jeroen P J
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format_se	Elektronische Aufsätze
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doi_str_mv	10.1186/1471-2164-13-696
author2-role	verfasserin
title_sort	<it<de novo</it< reconstruction of the <it<toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding rnas
callnumber	TP248.13-248.65
title_auth	<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
abstract	<p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p<
abstractGer	<p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p<
abstract_unstemmed	<p<Abstract</p< <p<Background</p< <p<Accurate gene model predictions and annotation of alternative splicing events are imperative for genomic studies in organisms that contain genes with multiple exons. Currently most gene models for the intracellular parasite, <it<Toxoplasma gondii</it<, are based on computer model predictions without cDNA sequence verification. Additionally, the nature and extent of alternative splicing in <it<Toxoplasma gondii</it< is unknown. In this study, we used <it<de novo</it< transcript assembly and the published type II (ME49) genomic sequence to quantify the extent of alternative splicing in <it<Toxoplasma</it< and to improve the current <it<Toxoplasma</it< gene annotations.</p< <p<Results</p< <p<We used high-throughput RNA-sequencing data to assemble full-length transcripts, independently of a reference genome, followed by gene annotation based on the ME49 genome. We assembled 13,533 transcripts overlapping with known ME49 genes in ToxoDB and then used this set to; a) improve the annotation in the untranslated regions of ToxoDB genes, b) identify novel exons within protein-coding ToxoDB genes, and c) report on 50 previously unidentified alternatively spliced transcripts. Additionally, we assembled a set of 2,930 transcripts not overlapping with any known ME49 genes in ToxoDB. From this set, we have identified 118 new ME49 genes, 18 novel <it<Toxoplasma</it< genes, and putative non-coding RNAs.</p< <p<Conclusion</p< <p<RNA-seq data and <it<de novo</it< transcript assembly provide a robust way to update incompletely annotated genomes, like the <it<Toxoplasma</it< genome. We have used RNA-seq to improve the annotation of several <it<Toxoplasma</it< genes, identify alternatively spliced genes, novel genes, novel exons, and putative non-coding RNAs.</p<
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title_short	<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs
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<it<De novo</it< reconstruction of the <it<Toxoplasma gondii</it< transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs

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