Exploration of alternative splicing events in ten different grapevine cultivars

Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compare...
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Autor*in:	Potenza, Emilio [verfasserIn] Racchi, Milvia Luisa Sterck, Lieven Coller, Emanuela Asquini, Elisa Tosatto, Silvio C. E. Velasco, Riccardo Van de Peer, Yves Cestaro, Alessandro

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2015

Schlagwörter:	Alternative splicing Vitis vinifera RNA-seq Stochastic noise

Anmerkung:	© Potenza et al. 2015

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 16(2015), 1 vom: 17. Sept.
Übergeordnetes Werk:	volume:16 ; year:2015 ; number:1 ; day:17 ; month:09

Links:	Volltext

DOI / URN:	10.1186/s12864-015-1922-5

Katalog-ID:	SPR027110494

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520			\|a Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars.
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matchkey_str	article:14712164:2015----::xlrtooatraiepiigvnsnedfee
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allfields	10.1186/s12864-015-1922-5 doi (DE-627)SPR027110494 (SPR)s12864-015-1922-5-e DE-627 ger DE-627 rakwb eng Potenza, Emilio verfasserin aut Exploration of alternative splicing events in ten different grapevine cultivars 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Potenza et al. 2015 Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213 Racchi, Milvia Luisa aut Sterck, Lieven aut Coller, Emanuela aut Asquini, Elisa aut Tosatto, Silvio C. E. aut Velasco, Riccardo aut Van de Peer, Yves aut Cestaro, Alessandro aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 17. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:17 month:09 https://dx.doi.org/10.1186/s12864-015-1922-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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 16 2015 1 17 09
spelling	10.1186/s12864-015-1922-5 doi (DE-627)SPR027110494 (SPR)s12864-015-1922-5-e DE-627 ger DE-627 rakwb eng Potenza, Emilio verfasserin aut Exploration of alternative splicing events in ten different grapevine cultivars 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Potenza et al. 2015 Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213 Racchi, Milvia Luisa aut Sterck, Lieven aut Coller, Emanuela aut Asquini, Elisa aut Tosatto, Silvio C. E. aut Velasco, Riccardo aut Van de Peer, Yves aut Cestaro, Alessandro aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 17. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:17 month:09 https://dx.doi.org/10.1186/s12864-015-1922-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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 16 2015 1 17 09
allfields_unstemmed	10.1186/s12864-015-1922-5 doi (DE-627)SPR027110494 (SPR)s12864-015-1922-5-e DE-627 ger DE-627 rakwb eng Potenza, Emilio verfasserin aut Exploration of alternative splicing events in ten different grapevine cultivars 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Potenza et al. 2015 Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213 Racchi, Milvia Luisa aut Sterck, Lieven aut Coller, Emanuela aut Asquini, Elisa aut Tosatto, Silvio C. E. aut Velasco, Riccardo aut Van de Peer, Yves aut Cestaro, Alessandro aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 17. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:17 month:09 https://dx.doi.org/10.1186/s12864-015-1922-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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 16 2015 1 17 09
allfieldsGer	10.1186/s12864-015-1922-5 doi (DE-627)SPR027110494 (SPR)s12864-015-1922-5-e DE-627 ger DE-627 rakwb eng Potenza, Emilio verfasserin aut Exploration of alternative splicing events in ten different grapevine cultivars 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Potenza et al. 2015 Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213 Racchi, Milvia Luisa aut Sterck, Lieven aut Coller, Emanuela aut Asquini, Elisa aut Tosatto, Silvio C. E. aut Velasco, Riccardo aut Van de Peer, Yves aut Cestaro, Alessandro aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 17. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:17 month:09 https://dx.doi.org/10.1186/s12864-015-1922-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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 16 2015 1 17 09
allfieldsSound	10.1186/s12864-015-1922-5 doi (DE-627)SPR027110494 (SPR)s12864-015-1922-5-e DE-627 ger DE-627 rakwb eng Potenza, Emilio verfasserin aut Exploration of alternative splicing events in ten different grapevine cultivars 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Potenza et al. 2015 Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213 Racchi, Milvia Luisa aut Sterck, Lieven aut Coller, Emanuela aut Asquini, Elisa aut Tosatto, Silvio C. E. aut Velasco, Riccardo aut Van de Peer, Yves aut Cestaro, Alessandro aut Enthalten in BMC genomics London : BioMed Central, 2000 16(2015), 1 vom: 17. Sept. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:16 year:2015 number:1 day:17 month:09 https://dx.doi.org/10.1186/s12864-015-1922-5 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER 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 16 2015 1 17 09
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source	Enthalten in BMC genomics 16(2015), 1 vom: 17. Sept. volume:16 year:2015 number:1 day:17 month:09
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author	Potenza, Emilio
spellingShingle	Potenza, Emilio misc Alternative splicing misc Vitis vinifera misc RNA-seq misc Stochastic noise Exploration of alternative splicing events in ten different grapevine cultivars
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topic_title	Exploration of alternative splicing events in ten different grapevine cultivars Alternative splicing (dpeaa)DE-He213 Vitis vinifera (dpeaa)DE-He213 RNA-seq (dpeaa)DE-He213 Stochastic noise (dpeaa)DE-He213
topic	misc Alternative splicing misc Vitis vinifera misc RNA-seq misc Stochastic noise
topic_unstemmed	misc Alternative splicing misc Vitis vinifera misc RNA-seq misc Stochastic noise
topic_browse	misc Alternative splicing misc Vitis vinifera misc RNA-seq misc Stochastic noise
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title	Exploration of alternative splicing events in ten different grapevine cultivars
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title_full	Exploration of alternative splicing events in ten different grapevine cultivars
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author_browse	Potenza, Emilio Racchi, Milvia Luisa Sterck, Lieven Coller, Emanuela Asquini, Elisa Tosatto, Silvio C. E. Velasco, Riccardo Van de Peer, Yves Cestaro, Alessandro
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doi_str_mv	10.1186/s12864-015-1922-5
title_sort	exploration of alternative splicing events in ten different grapevine cultivars
title_auth	Exploration of alternative splicing events in ten different grapevine cultivars
abstract	Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. © Potenza et al. 2015
abstractGer	Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. © Potenza et al. 2015
abstract_unstemmed	Background The complex dynamics of gene regulation in plants are still far from being fully understood. Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. However, AS seems to be extensively conserved among the 10 cultivars. © Potenza et al. 2015
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title_short	Exploration of alternative splicing events in ten different grapevine cultivars
url	https://dx.doi.org/10.1186/s12864-015-1922-5
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author2	Racchi, Milvia Luisa Sterck, Lieven Coller, Emanuela Asquini, Elisa Tosatto, Silvio C. E. Velasco, Riccardo Van de Peer, Yves Cestaro, Alessandro
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Among many factors involved, alternative splicing (AS) in particular is one of the least well documented. For many years, AS has been considered of less relevant in plants, especially when compared to animals, however, since the introduction of next generation sequencing techniques the number of plant genes believed to be alternatively spliced has increased exponentially. Results Here, we performed a comprehensive high-throughput transcript sequencing of ten different grapevine cultivars, which resulted in the first high coverage atlas of the grape berry transcriptome. We also developed findAS, a software tool for the analysis of alternatively spliced junctions. We demonstrate that at least 44 % of multi-exonic genes undergo AS and a large number of low abundance splice variants is present within the 131.622 splice junctions we have annotated from Pinot noir. Conclusions Our analysis shows that ~70 % of AS events have relatively low expression levels, furthermore alternative splice sites seem to be enriched near the constitutive ones in some extent showing the noise of the splicing mechanisms. 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Exploration of alternative splicing events in ten different grapevine cultivars

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