The draft genome of sweet orange (Citrus sinensis).
Identifieur interne : 000C95 ( Main/Exploration ); précédent : 000C94; suivant : 000C96The draft genome of sweet orange (Citrus sinensis).
Auteurs : Qiang Xu [République populaire de Chine] ; Ling-Ling Chen ; Xiaoan Ruan ; Dijun Chen ; Andan Zhu ; Chunli Chen ; Denis Bertrand ; Wen-Biao Jiao ; Bao-Hai Hao ; Matthew P. Lyon ; Jiongjiong Chen ; Song Gao ; Feng Xing ; Hong Lan ; Ji-Wei Chang ; Xianhong Ge ; Yang Lei ; Qun Hu ; Yin Miao ; Lun Wang ; Shixin Xiao ; Manosh Kumar Biswas ; Wenfang Zeng ; Fei Guo ; Hongbo Cao ; Xiaoming Yang ; Xi-Wen Xu ; Yun-Jiang Cheng ; Juan Xu ; Ji-Hong Liu ; Oscar Junhong Luo ; Zhonghui Tang ; Wen-Wu Guo ; Hanhui Kuang ; Hong-Yu Zhang ; Mikeal L. Roose ; Niranjan Nagarajan ; Xiu-Xin Deng ; Yijun RuanSource :
- Nature genetics [ 1546-1718 ] ; 2013.
English descriptors
- KwdEn :
- Chimera, Chromosome Mapping, Citrus sinensis (genetics), Citrus sinensis (metabolism), Cluster Analysis, Computational Biology (methods), Evolution, Molecular, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Order, Genome, Plant, Heterozygote, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Phylogeny, Vitamins (metabolism).
- MESH :
- chemical , metabolism : Vitamins.
- genetics : Citrus sinensis.
- metabolism : Citrus sinensis.
- methods : Computational Biology.
- Chimera, Chromosome Mapping, Cluster Analysis, Evolution, Molecular, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Order, Genome, Plant, Heterozygote, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Phylogeny.
Abstract
Oranges are an important nutritional source for human health and have immense economic value. Here we present a comprehensive analysis of the draft genome of sweet orange (Citrus sinensis). The assembled sequence covers 87.3% of the estimated orange genome, which is relatively compact, as 20% is composed of repetitive elements. We predicted 29,445 protein-coding genes, half of which are in the heterozygous state. With additional sequencing of two more citrus species and comparative analyses of seven citrus genomes, we present evidence to suggest that sweet orange originated from a backcross hybrid between pummelo and mandarin. Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future.
DOI: 10.1038/ng.2472
PubMed: 23179022
Affiliations:
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Le document en format XML
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Lyon</name></author><author><name sortKey="Chen, Jiongjiong" sort="Chen, Jiongjiong" uniqKey="Chen J" first="Jiongjiong" last="Chen">Jiongjiong Chen</name></author><author><name sortKey="Gao, Song" sort="Gao, Song" uniqKey="Gao S" first="Song" last="Gao">Song Gao</name></author><author><name sortKey="Xing, Feng" sort="Xing, Feng" uniqKey="Xing F" first="Feng" last="Xing">Feng Xing</name></author><author><name sortKey="Lan, Hong" sort="Lan, Hong" uniqKey="Lan H" first="Hong" last="Lan">Hong Lan</name></author><author><name sortKey="Chang, Ji Wei" sort="Chang, Ji Wei" uniqKey="Chang J" first="Ji-Wei" last="Chang">Ji-Wei Chang</name></author><author><name sortKey="Ge, Xianhong" sort="Ge, Xianhong" uniqKey="Ge X" first="Xianhong" last="Ge">Xianhong Ge</name></author><author><name sortKey="Lei, Yang" sort="Lei, Yang" uniqKey="Lei Y" first="Yang" last="Lei">Yang Lei</name></author><author><name sortKey="Hu, Qun" sort="Hu, Qun" uniqKey="Hu Q" first="Qun" last="Hu">Qun Hu</name></author><author><name sortKey="Miao, Yin" sort="Miao, Yin" uniqKey="Miao Y" first="Yin" last="Miao">Yin Miao</name></author><author><name sortKey="Wang, Lun" sort="Wang, Lun" uniqKey="Wang L" first="Lun" last="Wang">Lun Wang</name></author><author><name sortKey="Xiao, Shixin" sort="Xiao, Shixin" uniqKey="Xiao S" first="Shixin" last="Xiao">Shixin Xiao</name></author><author><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name></author><author><name sortKey="Zeng, Wenfang" sort="Zeng, Wenfang" uniqKey="Zeng W" first="Wenfang" last="Zeng">Wenfang Zeng</name></author><author><name sortKey="Guo, Fei" sort="Guo, Fei" uniqKey="Guo F" first="Fei" last="Guo">Fei Guo</name></author><author><name sortKey="Cao, Hongbo" sort="Cao, Hongbo" uniqKey="Cao H" first="Hongbo" last="Cao">Hongbo Cao</name></author><author><name sortKey="Yang, Xiaoming" sort="Yang, Xiaoming" uniqKey="Yang X" first="Xiaoming" last="Yang">Xiaoming Yang</name></author><author><name sortKey="Xu, Xi Wen" sort="Xu, Xi Wen" uniqKey="Xu X" first="Xi-Wen" last="Xu">Xi-Wen Xu</name></author><author><name sortKey="Cheng, Yun Jiang" sort="Cheng, Yun Jiang" uniqKey="Cheng Y" first="Yun-Jiang" last="Cheng">Yun-Jiang Cheng</name></author><author><name sortKey="Xu, Juan" sort="Xu, Juan" uniqKey="Xu J" first="Juan" last="Xu">Juan Xu</name></author><author><name sortKey="Liu, Ji Hong" sort="Liu, Ji Hong" uniqKey="Liu J" first="Ji-Hong" last="Liu">Ji-Hong Liu</name></author><author><name sortKey="Luo, Oscar Junhong" sort="Luo, Oscar Junhong" uniqKey="Luo O" first="Oscar Junhong" last="Luo">Oscar Junhong Luo</name></author><author><name sortKey="Tang, Zhonghui" sort="Tang, Zhonghui" uniqKey="Tang Z" first="Zhonghui" last="Tang">Zhonghui Tang</name></author><author><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name></author><author><name sortKey="Kuang, Hanhui" sort="Kuang, Hanhui" uniqKey="Kuang H" first="Hanhui" last="Kuang">Hanhui Kuang</name></author><author><name sortKey="Zhang, Hong Yu" sort="Zhang, Hong Yu" uniqKey="Zhang H" first="Hong-Yu" last="Zhang">Hong-Yu Zhang</name></author><author><name sortKey="Roose, Mikeal L" sort="Roose, Mikeal L" uniqKey="Roose M" first="Mikeal L" last="Roose">Mikeal L. Roose</name></author><author><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name></author><author><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name></author><author><name sortKey="Ruan, Yijun" sort="Ruan, Yijun" uniqKey="Ruan Y" first="Yijun" last="Ruan">Yijun Ruan</name></author></analytic><series><title level="j">Nature genetics</title><idno type="eISSN">1546-1718</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chimera</term><term>Chromosome Mapping</term><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (metabolism)</term><term>Cluster Analysis</term><term>Computational Biology (methods)</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Order</term><term>Genome, Plant</term><term>Heterozygote</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Vitamins (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Vitamins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chimera</term><term>Chromosome Mapping</term><term>Cluster Analysis</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Order</term><term>Genome, Plant</term><term>Heterozygote</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Data</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Oranges are an important nutritional source for human health and have immense economic value. Here we present a comprehensive analysis of the draft genome of sweet orange (Citrus sinensis). The assembled sequence covers 87.3% of the estimated orange genome, which is relatively compact, as 20% is composed of repetitive elements. We predicted 29,445 protein-coding genes, half of which are in the heterozygous state. With additional sequencing of two more citrus species and comparative analyses of seven citrus genomes, we present evidence to suggest that sweet orange originated from a backcross hybrid between pummelo and mandarin. Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Bertrand, Denis" sort="Bertrand, Denis" uniqKey="Bertrand D" first="Denis" last="Bertrand">Denis Bertrand</name><name sortKey="Biswas, Manosh Kumar" sort="Biswas, Manosh Kumar" uniqKey="Biswas M" first="Manosh Kumar" last="Biswas">Manosh Kumar Biswas</name><name sortKey="Cao, Hongbo" sort="Cao, Hongbo" uniqKey="Cao H" first="Hongbo" last="Cao">Hongbo Cao</name><name sortKey="Chang, Ji Wei" sort="Chang, Ji Wei" uniqKey="Chang J" first="Ji-Wei" last="Chang">Ji-Wei Chang</name><name sortKey="Chen, Chunli" sort="Chen, Chunli" uniqKey="Chen C" first="Chunli" last="Chen">Chunli Chen</name><name sortKey="Chen, Dijun" sort="Chen, Dijun" uniqKey="Chen D" first="Dijun" last="Chen">Dijun Chen</name><name sortKey="Chen, Jiongjiong" sort="Chen, Jiongjiong" uniqKey="Chen J" first="Jiongjiong" last="Chen">Jiongjiong Chen</name><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><name sortKey="Cheng, Yun Jiang" sort="Cheng, Yun Jiang" uniqKey="Cheng Y" first="Yun-Jiang" last="Cheng">Yun-Jiang Cheng</name><name sortKey="Deng, Xiu Xin" sort="Deng, Xiu Xin" uniqKey="Deng X" first="Xiu-Xin" last="Deng">Xiu-Xin Deng</name><name sortKey="Gao, Song" sort="Gao, Song" uniqKey="Gao S" first="Song" last="Gao">Song Gao</name><name sortKey="Ge, Xianhong" sort="Ge, Xianhong" uniqKey="Ge X" first="Xianhong" last="Ge">Xianhong Ge</name><name sortKey="Guo, Fei" sort="Guo, Fei" uniqKey="Guo F" first="Fei" last="Guo">Fei Guo</name><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><name sortKey="Hao, Bao Hai" sort="Hao, Bao Hai" uniqKey="Hao B" first="Bao-Hai" last="Hao">Bao-Hai Hao</name><name sortKey="Hu, Qun" sort="Hu, Qun" uniqKey="Hu Q" first="Qun" last="Hu">Qun Hu</name><name sortKey="Jiao, Wen Biao" sort="Jiao, Wen Biao" uniqKey="Jiao W" first="Wen-Biao" last="Jiao">Wen-Biao Jiao</name><name sortKey="Kuang, Hanhui" sort="Kuang, Hanhui" uniqKey="Kuang H" first="Hanhui" last="Kuang">Hanhui Kuang</name><name sortKey="Lan, Hong" sort="Lan, Hong" uniqKey="Lan H" first="Hong" last="Lan">Hong Lan</name><name sortKey="Lei, Yang" sort="Lei, Yang" uniqKey="Lei Y" first="Yang" last="Lei">Yang Lei</name><name sortKey="Liu, Ji Hong" sort="Liu, Ji Hong" uniqKey="Liu J" first="Ji-Hong" last="Liu">Ji-Hong Liu</name><name sortKey="Luo, Oscar Junhong" sort="Luo, Oscar Junhong" uniqKey="Luo O" first="Oscar Junhong" last="Luo">Oscar Junhong Luo</name><name sortKey="Lyon, Matthew P" sort="Lyon, Matthew P" uniqKey="Lyon M" first="Matthew P" last="Lyon">Matthew P. Lyon</name><name sortKey="Miao, Yin" sort="Miao, Yin" uniqKey="Miao Y" first="Yin" last="Miao">Yin Miao</name><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name><name sortKey="Roose, Mikeal L" sort="Roose, Mikeal L" uniqKey="Roose M" first="Mikeal L" last="Roose">Mikeal L. Roose</name><name sortKey="Ruan, Xiaoan" sort="Ruan, Xiaoan" uniqKey="Ruan X" first="Xiaoan" last="Ruan">Xiaoan Ruan</name><name sortKey="Ruan, Yijun" sort="Ruan, Yijun" uniqKey="Ruan Y" first="Yijun" last="Ruan">Yijun Ruan</name><name sortKey="Tang, Zhonghui" sort="Tang, Zhonghui" uniqKey="Tang Z" first="Zhonghui" last="Tang">Zhonghui Tang</name><name sortKey="Wang, Lun" sort="Wang, Lun" uniqKey="Wang L" first="Lun" last="Wang">Lun Wang</name><name sortKey="Xiao, Shixin" sort="Xiao, Shixin" uniqKey="Xiao S" first="Shixin" last="Xiao">Shixin Xiao</name><name sortKey="Xing, Feng" sort="Xing, Feng" uniqKey="Xing F" first="Feng" last="Xing">Feng Xing</name><name sortKey="Xu, Juan" sort="Xu, Juan" uniqKey="Xu J" first="Juan" last="Xu">Juan Xu</name><name sortKey="Xu, Xi Wen" sort="Xu, Xi Wen" uniqKey="Xu X" first="Xi-Wen" last="Xu">Xi-Wen Xu</name><name sortKey="Yang, Xiaoming" sort="Yang, Xiaoming" uniqKey="Yang X" first="Xiaoming" last="Yang">Xiaoming Yang</name><name sortKey="Zeng, Wenfang" sort="Zeng, Wenfang" uniqKey="Zeng W" first="Wenfang" last="Zeng">Wenfang Zeng</name><name sortKey="Zhang, Hong Yu" sort="Zhang, Hong Yu" uniqKey="Zhang H" first="Hong-Yu" last="Zhang">Hong-Yu Zhang</name><name sortKey="Zhu, Andan" sort="Zhu, Andan" uniqKey="Zhu A" first="Andan" last="Zhu">Andan Zhu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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