Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice

Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. How...
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Autor*in:	Huang He [verfasserIn] Yan-Fei Zhou [verfasserIn] Yu-Wei Yang [verfasserIn] Zhi Zhang [verfasserIn] Meng-Qi Lei [verfasserIn] Yan-Zhao Feng [verfasserIn] Yu-Chan Zhang [verfasserIn] Yue-Qin Chen [verfasserIn] Jian-Ping Lian [verfasserIn] Yang Yu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 22(2021), 9, p 4742
Übergeordnetes Werk:	volume:22 ; year:2021 ; number:9, p 4742

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms22094742

Katalog-ID:	DOAJ06106257X

Internformat


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520			\|a Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
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allfields	10.3390/ijms22094742 doi (DE-627)DOAJ06106257X (DE-599)DOAJ6d90f20e26094cb4b3007f5da6d3f745 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Huang He verfasserin aut Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice. agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice Biology (General) Chemistry Yan-Fei Zhou verfasserin aut Yu-Wei Yang verfasserin aut Zhi Zhang verfasserin aut Meng-Qi Lei verfasserin aut Yan-Zhao Feng verfasserin aut Yu-Chan Zhang verfasserin aut Yue-Qin Chen verfasserin aut Jian-Ping Lian verfasserin aut Yang Yu verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 9, p 4742 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:9, p 4742 https://doi.org/10.3390/ijms22094742 kostenfrei https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 kostenfrei https://www.mdpi.com/1422-0067/22/9/4742 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 22 2021 9, p 4742
spelling	10.3390/ijms22094742 doi (DE-627)DOAJ06106257X (DE-599)DOAJ6d90f20e26094cb4b3007f5da6d3f745 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Huang He verfasserin aut Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice. agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice Biology (General) Chemistry Yan-Fei Zhou verfasserin aut Yu-Wei Yang verfasserin aut Zhi Zhang verfasserin aut Meng-Qi Lei verfasserin aut Yan-Zhao Feng verfasserin aut Yu-Chan Zhang verfasserin aut Yue-Qin Chen verfasserin aut Jian-Ping Lian verfasserin aut Yang Yu verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 9, p 4742 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:9, p 4742 https://doi.org/10.3390/ijms22094742 kostenfrei https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 kostenfrei https://www.mdpi.com/1422-0067/22/9/4742 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 22 2021 9, p 4742
allfields_unstemmed	10.3390/ijms22094742 doi (DE-627)DOAJ06106257X (DE-599)DOAJ6d90f20e26094cb4b3007f5da6d3f745 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Huang He verfasserin aut Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice. agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice Biology (General) Chemistry Yan-Fei Zhou verfasserin aut Yu-Wei Yang verfasserin aut Zhi Zhang verfasserin aut Meng-Qi Lei verfasserin aut Yan-Zhao Feng verfasserin aut Yu-Chan Zhang verfasserin aut Yue-Qin Chen verfasserin aut Jian-Ping Lian verfasserin aut Yang Yu verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 9, p 4742 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:9, p 4742 https://doi.org/10.3390/ijms22094742 kostenfrei https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 kostenfrei https://www.mdpi.com/1422-0067/22/9/4742 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 22 2021 9, p 4742
allfieldsGer	10.3390/ijms22094742 doi (DE-627)DOAJ06106257X (DE-599)DOAJ6d90f20e26094cb4b3007f5da6d3f745 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Huang He verfasserin aut Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice. agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice Biology (General) Chemistry Yan-Fei Zhou verfasserin aut Yu-Wei Yang verfasserin aut Zhi Zhang verfasserin aut Meng-Qi Lei verfasserin aut Yan-Zhao Feng verfasserin aut Yu-Chan Zhang verfasserin aut Yue-Qin Chen verfasserin aut Jian-Ping Lian verfasserin aut Yang Yu verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 9, p 4742 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:9, p 4742 https://doi.org/10.3390/ijms22094742 kostenfrei https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 kostenfrei https://www.mdpi.com/1422-0067/22/9/4742 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 22 2021 9, p 4742
allfieldsSound	10.3390/ijms22094742 doi (DE-627)DOAJ06106257X (DE-599)DOAJ6d90f20e26094cb4b3007f5da6d3f745 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Huang He verfasserin aut Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice. agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice Biology (General) Chemistry Yan-Fei Zhou verfasserin aut Yu-Wei Yang verfasserin aut Zhi Zhang verfasserin aut Meng-Qi Lei verfasserin aut Yan-Zhao Feng verfasserin aut Yu-Chan Zhang verfasserin aut Yue-Qin Chen verfasserin aut Jian-Ping Lian verfasserin aut Yang Yu verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 9, p 4742 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:9, p 4742 https://doi.org/10.3390/ijms22094742 kostenfrei https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 kostenfrei https://www.mdpi.com/1422-0067/22/9/4742 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 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_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 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 22 2021 9, p 4742
language	English
source	In International Journal of Molecular Sciences 22(2021), 9, p 4742 volume:22 year:2021 number:9, p 4742
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callnumber-first	Q - Science
author	Huang He
spellingShingle	Huang He misc QH301-705.5 misc QD1-999 misc agronomic traits misc conservation misc crop domestication misc cultivated rice misc lncRNAs misc wild rice misc Biology (General) misc Chemistry Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice
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topic_title	QH301-705.5 QD1-999 Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice agronomic traits conservation crop domestication cultivated rice lncRNAs wild rice
topic	misc QH301-705.5 misc QD1-999 misc agronomic traits misc conservation misc crop domestication misc cultivated rice misc lncRNAs misc wild rice misc Biology (General) misc Chemistry
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title	Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice
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title_auth	Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice
abstract	Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
abstractGer	Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
abstract_unstemmed	Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
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container_issue	9, p 4742
title_short	Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice
url	https://doi.org/10.3390/ijms22094742 https://doaj.org/article/6d90f20e26094cb4b3007f5da6d3f745 https://www.mdpi.com/1422-0067/22/9/4742 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067
remote_bool	true
author2	Yan-Fei Zhou Yu-Wei Yang Zhi Zhang Meng-Qi Lei Yan-Zhao Feng Yu-Chan Zhang Yue-Qin Chen Jian-Ping Lian Yang Yu
author2Str	Yan-Fei Zhou Yu-Wei Yang Zhi Zhang Meng-Qi Lei Yan-Zhao Feng Yu-Chan Zhang Yue-Qin Chen Jian-Ping Lian Yang Yu
ppnlink	316340715
callnumber-subject	QH - Natural History and Biology
mediatype_str_mv	c
isOA_txt	true
hochschulschrift_bool	false
doi_str	10.3390/ijms22094742
callnumber-a	QH301-705.5
up_date	2024-07-03T18:37:26.220Z
_version_	1803584113186177024
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Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice <i<Oryza sativa</i< ssp. <i<japonica</i< and <i<O. sativa</i< ssp. <i<indica</i<, and their wild progenitor <i<O. rufipogon</i<. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in <i<O. rufipogon</i<, 2091 lncRNAs in <i<japonica</i< rice, and 2365 lncRNAs in <i<indica</i< rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. 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Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice

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