Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type

Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated b...
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Autor*in:	Xu, Qiang [verfasserIn] Liu, Yuanlong Zhu, Andan Wu, Xiaomeng Ye, Junli Yu, Keqin Guo, Wenwu Deng, Xiuxin

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2010

Schlagwörter:	Lycopene miRNA Family Sweet Orange sRNA Library sRNA Sequence

Anmerkung:	© Xu et al; licensee BioMed Central Ltd. 2010

Übergeordnetes Werk:	Enthalten in: BMC genomics - London : BioMed Central, 2000, 11(2010), 1 vom: 17. Apr.
Übergeordnetes Werk:	volume:11 ; year:2010 ; number:1 ; day:17 ; month:04

Links:	Volltext

DOI / URN:	10.1186/1471-2164-11-246

Katalog-ID:	SPR027052834

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520			\|a Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.
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700	1		\|a Liu, Yuanlong \|4 aut
700	1		\|a Zhu, Andan \|4 aut
700	1		\|a Wu, Xiaomeng \|4 aut
700	1		\|a Ye, Junli \|4 aut
700	1		\|a Yu, Keqin \|4 aut
700	1		\|a Guo, Wenwu \|4 aut
700	1		\|a Deng, Xiuxin \|4 aut
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912			\|a GBV_ILN_213
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allfields	10.1186/1471-2164-11-246 doi (DE-627)SPR027052834 (SPR)1471-2164-11-246-e DE-627 ger DE-627 rakwb eng Xu, Qiang verfasserin aut Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Xu et al; licensee BioMed Central Ltd. 2010 Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213 Liu, Yuanlong aut Zhu, Andan aut Wu, Xiaomeng aut Ye, Junli aut Yu, Keqin aut Guo, Wenwu aut Deng, Xiuxin aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 17. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:17 month:04 https://dx.doi.org/10.1186/1471-2164-11-246 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 11 2010 1 17 04
spelling	10.1186/1471-2164-11-246 doi (DE-627)SPR027052834 (SPR)1471-2164-11-246-e DE-627 ger DE-627 rakwb eng Xu, Qiang verfasserin aut Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Xu et al; licensee BioMed Central Ltd. 2010 Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213 Liu, Yuanlong aut Zhu, Andan aut Wu, Xiaomeng aut Ye, Junli aut Yu, Keqin aut Guo, Wenwu aut Deng, Xiuxin aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 17. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:17 month:04 https://dx.doi.org/10.1186/1471-2164-11-246 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 11 2010 1 17 04
allfields_unstemmed	10.1186/1471-2164-11-246 doi (DE-627)SPR027052834 (SPR)1471-2164-11-246-e DE-627 ger DE-627 rakwb eng Xu, Qiang verfasserin aut Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Xu et al; licensee BioMed Central Ltd. 2010 Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213 Liu, Yuanlong aut Zhu, Andan aut Wu, Xiaomeng aut Ye, Junli aut Yu, Keqin aut Guo, Wenwu aut Deng, Xiuxin aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 17. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:17 month:04 https://dx.doi.org/10.1186/1471-2164-11-246 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 11 2010 1 17 04
allfieldsGer	10.1186/1471-2164-11-246 doi (DE-627)SPR027052834 (SPR)1471-2164-11-246-e DE-627 ger DE-627 rakwb eng Xu, Qiang verfasserin aut Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Xu et al; licensee BioMed Central Ltd. 2010 Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213 Liu, Yuanlong aut Zhu, Andan aut Wu, Xiaomeng aut Ye, Junli aut Yu, Keqin aut Guo, Wenwu aut Deng, Xiuxin aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 17. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:17 month:04 https://dx.doi.org/10.1186/1471-2164-11-246 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 11 2010 1 17 04
allfieldsSound	10.1186/1471-2164-11-246 doi (DE-627)SPR027052834 (SPR)1471-2164-11-246-e DE-627 ger DE-627 rakwb eng Xu, Qiang verfasserin aut Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type 2010 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Xu et al; licensee BioMed Central Ltd. 2010 Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213 Liu, Yuanlong aut Zhu, Andan aut Wu, Xiaomeng aut Ye, Junli aut Yu, Keqin aut Guo, Wenwu aut Deng, Xiuxin aut Enthalten in BMC genomics London : BioMed Central, 2000 11(2010), 1 vom: 17. Apr. (DE-627)326644954 (DE-600)2041499-7 1471-2164 nnns volume:11 year:2010 number:1 day:17 month:04 https://dx.doi.org/10.1186/1471-2164-11-246 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 11 2010 1 17 04
language	English
source	Enthalten in BMC genomics 11(2010), 1 vom: 17. Apr. volume:11 year:2010 number:1 day:17 month:04
sourceStr	Enthalten in BMC genomics 11(2010), 1 vom: 17. Apr. volume:11 year:2010 number:1 day:17 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Lycopene miRNA Family Sweet Orange sRNA Library sRNA Sequence
isfreeaccess_bool	true
container_title	BMC genomics
authorswithroles_txt_mv	Xu, Qiang @@aut@@ Liu, Yuanlong @@aut@@ Zhu, Andan @@aut@@ Wu, Xiaomeng @@aut@@ Ye, Junli @@aut@@ Yu, Keqin @@aut@@ Guo, Wenwu @@aut@@ Deng, Xiuxin @@aut@@
publishDateDaySort_date	2010-04-17T00:00:00Z
hierarchy_top_id	326644954
id	SPR027052834
language_de	englisch
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author	Xu, Qiang
spellingShingle	Xu, Qiang misc Lycopene misc miRNA Family misc Sweet Orange misc sRNA Library misc sRNA Sequence Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
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topic_title	Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type Lycopene (dpeaa)DE-He213 miRNA Family (dpeaa)DE-He213 Sweet Orange (dpeaa)DE-He213 sRNA Library (dpeaa)DE-He213 sRNA Sequence (dpeaa)DE-He213
topic	misc Lycopene misc miRNA Family misc Sweet Orange misc sRNA Library misc sRNA Sequence
topic_unstemmed	misc Lycopene misc miRNA Family misc Sweet Orange misc sRNA Library misc sRNA Sequence
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title	Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
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title_full	Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
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author_browse	Xu, Qiang Liu, Yuanlong Zhu, Andan Wu, Xiaomeng Ye, Junli Yu, Keqin Guo, Wenwu Deng, Xiuxin
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title_sort	discovery and comparative profiling of micrornas in a sweet orange red-flesh mutant and its wild type
title_auth	Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
abstract	Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. © Xu et al; licensee BioMed Central Ltd. 2010
abstractGer	Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. © Xu et al; licensee BioMed Central Ltd. 2010
abstract_unstemmed	Background Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far. Results We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT. Conclusion This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant. © Xu et al; licensee BioMed Central Ltd. 2010
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title_short	Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type
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author2	Liu, Yuanlong Zhu, Andan Wu, Xiaomeng Ye, Junli Yu, Keqin Guo, Wenwu Deng, Xiuxin
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