Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA-mediated transcript cleavage involved in somatic embryogenesis.
Identifieur interne : 000614 ( Main/Exploration ); précédent : 000613; suivant : 000615Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA-mediated transcript cleavage involved in somatic embryogenesis.
Auteurs : Xiao-Meng Wu [République populaire de Chine] ; Shu-Jun Kou ; Yuan-Long Liu ; Yan-Ni Fang ; Qiang Xu ; Wen-Wu GuoSource :
- Plant biotechnology journal [ 1467-7652 ] ; 2015.
English descriptors
- KwdEn :
- Citrus sinensis (embryology), Citrus sinensis (genetics), Gene Expression Regulation, Plant, Genome, Plant (genetics), High-Throughput Nucleotide Sequencing, MicroRNAs (genetics), Plant Somatic Embryogenesis Techniques, RNA Cleavage, RNA, Plant (genetics), RNA, Small Interfering (genetics), Sequence Analysis, RNA.
- MESH :
- chemical , genetics : MicroRNAs, RNA, Plant, RNA, Small Interfering.
- embryology : Citrus sinensis.
- genetics : Citrus sinensis, Genome, Plant.
- Gene Expression Regulation, Plant, High-Throughput Nucleotide Sequencing, Plant Somatic Embryogenesis Techniques, RNA Cleavage, Sequence Analysis, RNA.
Abstract
Somatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs and their target genes in nonembryogenic and embryogenic tissues of 'Valencia' sweet orange. By high-throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes. The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, miRNA- and siRNA-mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE.
DOI: 10.1111/pbi.12317
PubMed: 25615015
Affiliations:
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Long" uniqKey="Liu Y" first="Yuan-Long" last="Liu">Yuan-Long Liu</name></author><author><name sortKey="Fang, Yan Ni" sort="Fang, Yan Ni" uniqKey="Fang Y" first="Yan-Ni" last="Fang">Yan-Ni Fang</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</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></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25615015</idno><idno type="pmid">25615015</idno><idno type="doi">10.1111/pbi.12317</idno><idno type="wicri:Area/PubMed/Corpus">000200</idno><idno type="wicri:Area/PubMed/Curation">000200</idno><idno type="wicri:Area/PubMed/Checkpoint">000200</idno><idno type="wicri:Area/Ncbi/Merge">001986</idno><idno type="wicri:Area/Ncbi/Curation">001986</idno><idno type="wicri:Area/Ncbi/Checkpoint">001986</idno><idno 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Shu Jun" sort="Kou, Shu Jun" uniqKey="Kou S" first="Shu-Jun" last="Kou">Shu-Jun Kou</name></author><author><name sortKey="Liu, Yuan Long" sort="Liu, Yuan Long" uniqKey="Liu Y" first="Yuan-Long" last="Liu">Yuan-Long Liu</name></author><author><name sortKey="Fang, Yan Ni" sort="Fang, Yan Ni" uniqKey="Fang Y" first="Yan-Ni" last="Fang">Yan-Ni Fang</name></author><author><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</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></analytic><series><title level="j">Plant biotechnology journal</title><idno type="eISSN">1467-7652</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Citrus sinensis (embryology)</term><term>Citrus sinensis (genetics)</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant (genetics)</term><term>High-Throughput Nucleotide Sequencing</term><term>MicroRNAs (genetics)</term><term>Plant Somatic Embryogenesis Techniques</term><term>RNA Cleavage</term><term>RNA, Plant (genetics)</term><term>RNA, Small Interfering (genetics)</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Plant</term><term>RNA, Small Interfering</term></keywords><keywords scheme="MESH" qualifier="embryology" xml:lang="en"><term>Citrus sinensis</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Genome, Plant</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Plant Somatic Embryogenesis Techniques</term><term>RNA Cleavage</term><term>Sequence Analysis, RNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Somatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs and their target genes in nonembryogenic and embryogenic tissues of 'Valencia' sweet orange. By high-throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes. The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, miRNA- and siRNA-mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Fang, Yan Ni" sort="Fang, Yan Ni" uniqKey="Fang Y" first="Yan-Ni" last="Fang">Yan-Ni Fang</name><name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name><name sortKey="Kou, Shu Jun" sort="Kou, Shu Jun" uniqKey="Kou S" first="Shu-Jun" last="Kou">Shu-Jun Kou</name><name sortKey="Liu, Yuan Long" sort="Liu, Yuan Long" uniqKey="Liu Y" first="Yuan-Long" last="Liu">Yuan-Long Liu</name><name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Wu, Xiao Meng" sort="Wu, Xiao Meng" uniqKey="Wu X" first="Xiao-Meng" last="Wu">Xiao-Meng Wu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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