Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange
Identifieur interne : 000A59 ( Main/Exploration ); précédent : 000A58; suivant : 000A60Genome-wide comparison of microRNAs and their targeted transcripts among leaf, flower and fruit of sweet orange
Auteurs : Yuanlong Liu [République populaire de Chine] ; Lun Wang [République populaire de Chine] ; Dijun Chen [République populaire de Chine] ; Xiaomeng Wu [République populaire de Chine] ; Ding Huang [République populaire de Chine] ; Lingling Chen [République populaire de Chine] ; Li Li [États-Unis] ; Xiuxin Deng [République populaire de Chine] ; Qiang Xu [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2014.
English descriptors
- KwdEn :
- Base Sequence, Binding Sites, Chromosome Mapping, Citrus sinensis (genetics), Citrus sinensis (metabolism), Flowers (genetics), Flowers (metabolism), Fruit (genetics), Fruit (metabolism), Gene Expression Regulation, Plant, Genome, Plant, MicroRNAs (genetics), MicroRNAs (metabolism), Microsatellite Repeats, Molecular Sequence Annotation, Plant Leaves (genetics), Plant Leaves (metabolism), Plant Proteins (metabolism), RNA Interference, RNA, Messenger (genetics), RNA, Messenger (metabolism), RNA, Plant (genetics), RNA, Plant (metabolism), Sequence Analysis, RNA, Transcriptome.
- MESH :
- chemical , genetics : MicroRNAs, RNA, Messenger, RNA, Plant.
- genetics : Citrus sinensis, Flowers, Fruit, Plant Leaves.
- metabolism : Citrus sinensis, Flowers, Fruit, MicroRNAs, Plant Leaves, Plant Proteins, RNA, Messenger, RNA, Plant.
- Base Sequence, Binding Sites, Chromosome Mapping, Gene Expression Regulation, Plant, Genome, Plant, Microsatellite Repeats, Molecular Sequence Annotation, RNA Interference, Sequence Analysis, RNA, Transcriptome.
Abstract
In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant development. Here, we used a high-throughput sequencing approach to characterize the miRNAs and their targeted transcripts in the leaf, flower and fruit of sweet orange.
A total of 183 known miRNAs and 38 novel miRNAs were identified. An in-house script was used to identify all potential secondary siRNAs derived from miRNA-targeted transcripts using sRNA and degradome sequencing data. Genome mapping revealed that these miRNAs were evenly distributed across the genome with several small clusters, and 69 pre-miRNAs were co-localized with simple sequence repeats (SSRs). Noticeably, the loop size of pre-miR396c was influenced by the repeat number of CUU unit. The expression pattern of miRNAs among different tissues and developmental stages were further investigated by both qRT-PCR and RNA gel blotting. Interestingly, Csi-miR164 was highly expressed in fruit ripening stage, and was validated to target a NAC transcription factor. This study depicts a global picture of miRNAs and their target genes in the genome of sweet orange, and focused on the comparison among leaf, flower and fruit tissues.
This study provides a global view of miRNAs and their target genes in different tissue of sweet orange, and focused on the identification of miRNA involved in the regulation of fruit ripening. The results of this study lay a foundation for unraveling key regulators of orange fruit development and ripening on post-transcriptional level.
The online version of this article (doi:10.1186/1471-2164-15-695) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-15-695
PubMed: 25142253
PubMed Central: 4158063
Affiliations:
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Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Robert W. 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Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Lun" sort="Wang, Lun" uniqKey="Wang L" first="Lun" last="Wang">Lun Wang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Dijun" sort="Chen, Dijun" uniqKey="Chen D" first="Dijun" last="Chen">Dijun Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Xiaomeng" sort="Wu, Xiaomeng" uniqKey="Wu X" first="Xiaomeng" last="Wu">Xiaomeng Wu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Ding" sort="Huang, Ding" uniqKey="Huang D" first="Ding" last="Huang">Ding Huang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Lingling" sort="Chen, Lingling" uniqKey="Chen L" first="Lingling" last="Chen">Lingling Chen</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Li, Li" sort="Li, Li" uniqKey="Li L" first="Li" last="Li">Li Li</name><affiliation wicri:level="2"><nlm:aff id="Aff3">Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><wicri:cityArea>Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca</wicri:cityArea></affiliation></author><author><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan</wicri:regionArea><wicri:noRegion>Wuhan</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Chromosome Mapping</term><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (metabolism)</term><term>Flowers (genetics)</term><term>Flowers (metabolism)</term><term>Fruit (genetics)</term><term>Fruit (metabolism)</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>MicroRNAs (genetics)</term><term>MicroRNAs (metabolism)</term><term>Microsatellite Repeats</term><term>Molecular Sequence Annotation</term><term>Plant Leaves (genetics)</term><term>Plant Leaves (metabolism)</term><term>Plant Proteins (metabolism)</term><term>RNA Interference</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (metabolism)</term><term>RNA, Plant (genetics)</term><term>RNA, Plant (metabolism)</term><term>Sequence Analysis, RNA</term><term>Transcriptome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Flowers</term><term>Fruit</term><term>Plant Leaves</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Citrus sinensis</term><term>Flowers</term><term>Fruit</term><term>MicroRNAs</term><term>Plant Leaves</term><term>Plant Proteins</term><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Chromosome Mapping</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>Microsatellite Repeats</term><term>Molecular Sequence Annotation</term><term>RNA Interference</term><term>Sequence Analysis, RNA</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant development. Here, we used a high-throughput sequencing approach to characterize the miRNAs and their targeted transcripts in the leaf, flower and fruit of sweet orange.</p></sec><sec><title>Results</title><p>A total of 183 known miRNAs and 38 novel miRNAs were identified. An in-house script was used to identify all potential secondary siRNAs derived from miRNA-targeted transcripts using sRNA and degradome sequencing data. Genome mapping revealed that these miRNAs were evenly distributed across the genome with several small clusters, and 69 pre-miRNAs were co-localized with simple sequence repeats (SSRs). Noticeably, the loop size of pre-miR396c was influenced by the repeat number of CUU unit. The expression pattern of miRNAs among different tissues and developmental stages were further investigated by both qRT-PCR and RNA gel blotting. Interestingly, Csi-miR164 was highly expressed in fruit ripening stage, and was validated to target a NAC transcription factor. This study depicts a global picture of miRNAs and their target genes in the genome of sweet orange, and focused on the comparison among leaf, flower and fruit tissues.</p></sec><sec><title>Conclusions</title><p>This study provides a global view of miRNAs and their target genes in different tissue of sweet orange, and focused on the identification of miRNA involved in the regulation of fruit ripening. The results of this study lay a foundation for unraveling key regulators of orange fruit development and ripening on post-transcriptional level.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-15-695) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X Zhang</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Kiba, T" uniqKey="Kiba T">T Kiba</name></author><author><name sortKey="Woo, J" uniqKey="Woo J">J Woo</name></author><author><name sortKey="Ojo, T" uniqKey="Ojo T">T Ojo</name></author><author><name sortKey="Hafner, M" uniqKey="Hafner M">M Hafner</name></author><author><name sortKey="Tuschl, T" uniqKey="Tuschl T">T Tuschl</name></author><author><name sortKey="Chua, Nh" uniqKey="Chua N">NH Chua</name></author><author><name sortKey="Wang, Xj" uniqKey="Wang X">XJ Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Vn" uniqKey="Kim V">VN Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jin, Hl" uniqKey="Jin H">HL Jin</name></author><author><name sortKey="Zhang, Xm" uniqKey="Zhang X">XM Zhang</name></author><author><name sortKey="Zhao, Hw" uniqKey="Zhao H">HW Zhao</name></author><author><name sortKey="Gao, S" uniqKey="Gao S">S Gao</name></author><author><name sortKey="Wang, Wc" uniqKey="Wang W">WC Wang</name></author><author><name sortKey="Katiyar Agarwal, S" uniqKey="Katiyar Agarwal S">S Katiyar-Agarwal</name></author><author><name sortKey="Huang, Hd" uniqKey="Huang H">HD 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Chine</li><li>États-Unis</li></country><region><li>État de New York</li></region></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Yuanlong" sort="Liu, Yuanlong" uniqKey="Liu Y" first="Yuanlong" last="Liu">Yuanlong Liu</name></noRegion><name sortKey="Chen, Dijun" sort="Chen, Dijun" uniqKey="Chen D" first="Dijun" last="Chen">Dijun Chen</name><name sortKey="Chen, Lingling" sort="Chen, Lingling" uniqKey="Chen L" first="Lingling" last="Chen">Lingling Chen</name><name sortKey="Deng, Xiuxin" sort="Deng, Xiuxin" uniqKey="Deng X" first="Xiuxin" last="Deng">Xiuxin Deng</name><name sortKey="Huang, Ding" sort="Huang, Ding" uniqKey="Huang D" first="Ding" last="Huang">Ding Huang</name><name sortKey="Wang, Lun" sort="Wang, Lun" uniqKey="Wang L" first="Lun" last="Wang">Lun Wang</name><name sortKey="Wu, Xiaomeng" sort="Wu, Xiaomeng" uniqKey="Wu X" first="Xiaomeng" last="Wu">Xiaomeng Wu</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></country><country name="États-Unis"><region name="État de New York"><name sortKey="Li, Li" sort="Li, Li" uniqKey="Li L" first="Li" last="Li">Li Li</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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