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High-throughput sequencing and degradome analysis reveal altered expression of miRNAs and their targets in a male-sterile cybrid pummelo (Citrus grandis)

Identifieur interne : 000180 ( Main/Exploration ); précédent : 000179; suivant : 000181

High-throughput sequencing and degradome analysis reveal altered expression of miRNAs and their targets in a male-sterile cybrid pummelo (Citrus grandis)

Auteurs : Yan-Ni Fang [République populaire de Chine] ; Bei-Bei Zheng [République populaire de Chine] ; Lun Wang [République populaire de Chine] ; Wei Yang [République populaire de Chine] ; Xiao-Meng Wu [République populaire de Chine] ; Qiang Xu [République populaire de Chine] ; Wen-Wu Guo [République populaire de Chine]

Source :

RBID : PMC:4979119

Abstract

Background

G1 + HBP is a male sterile cybrid line with nuclear genome from Hirado Buntan pummelo (C. grandis Osbeck) (HBP) and mitochondrial genome from “Guoqing No.1” (G1, Satsuma mandarin), which provides a good opportunity to study male sterility and nuclear-cytoplasmic cross talk in citrus. High-throughput sRNA and degradome sequencing were applied to identify miRNAs and their targets in G1 + HBP and its fertile type HBP during reproductive development.

Results

A total of 184 known miRNAs, 22 novel miRNAs and 86 target genes were identified. Some of the targets are transcription factors involved in floral development, such as auxin response factors (ARFs), SQUAMOSA promoter binding protein box (SBP-box), MYB, basic region-leucine zipper (bZIP), APETALA2 (AP2) and transport inhibitor response 1 (TIR1). Eight target genes were confirmed to be sliced by corresponding miRNAs using 5’ RACE technology. Based on the sequencing abundance, 42 differentially expressed miRNAs between sterile line G1 + HBP and fertile line HBP were identified. Differential expression of miRNAs and their target genes between two lines was validated by quantitative RT-PCR, and reciprocal expression patterns between some miRNAs and their targets were demonstrated. The regulatory mechanism of miR167a was investigated by yeast one-hybrid and dual-luciferase assays that one dehydrate responsive element binding (DREB) transcription factor binds to miR167a promoter and transcriptionally repress miR167 expression.

Conclusion

Our study reveals the altered expression of miRNAs and their target genes in a male sterile line of pummelo and highlights that miRNA regulatory network may be involved in floral bud development and cytoplasmic male sterility in citrus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2882-0) contains supplementary material, which is available to authorized users.


Url:
DOI: 10.1186/s12864-016-2882-0
PubMed: 27506907
PubMed Central: 4979119


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<title>Background</title>
<p>G1 + HBP is a male sterile cybrid line with nuclear genome from Hirado Buntan pummelo (
<italic>C. grandis</italic>
Osbeck) (HBP) and mitochondrial genome from “Guoqing No.1” (G1, Satsuma mandarin), which provides a good opportunity to study male sterility and nuclear-cytoplasmic cross talk in citrus. High-throughput sRNA and degradome sequencing were applied to identify miRNAs and their targets in G1 + HBP and its fertile type HBP during reproductive development.</p>
</sec>
<sec>
<title>Results</title>
<p>A total of 184 known miRNAs, 22 novel miRNAs and 86 target genes were identified. Some of the targets are transcription factors involved in floral development, such as auxin response factors (
<italic>ARFs</italic>
),
<italic>SQUAMOSA</italic>
promoter binding protein box (SBP-box),
<italic>MYB</italic>
, basic region-leucine zipper (
<italic>bZIP</italic>
),
<italic>APETALA2</italic>
(
<italic>AP2</italic>
) and transport inhibitor response 1 (
<italic>TIR1</italic>
). Eight target genes were confirmed to be sliced by corresponding miRNAs using 5’ RACE technology. Based on the sequencing abundance, 42 differentially expressed miRNAs between sterile line G1 + HBP and fertile line HBP were identified. Differential expression of miRNAs and their target genes between two lines was validated by quantitative RT-PCR, and reciprocal expression patterns between some miRNAs and their targets were demonstrated. The regulatory mechanism of miR167a was investigated by yeast one-hybrid and dual-luciferase assays that one dehydrate responsive element binding (DREB) transcription factor binds to miR167a promoter and transcriptionally repress miR167 expression.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>Our study reveals the altered expression of miRNAs and their target genes in a male sterile line of pummelo and highlights that miRNA regulatory network may be involved in floral bud development and cytoplasmic male sterility in citrus.</p>
</sec>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-016-2882-0) contains supplementary material, which is available to authorized users.</p>
</sec>
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<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
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<name sortKey="Fang, Yan Ni" sort="Fang, Yan Ni" uniqKey="Fang Y" first="Yan-Ni" last="Fang">Yan-Ni Fang</name>
</noRegion>
<name sortKey="Guo, Wen Wu" sort="Guo, Wen Wu" uniqKey="Guo W" first="Wen-Wu" last="Guo">Wen-Wu Guo</name>
<name sortKey="Wang, Lun" sort="Wang, Lun" uniqKey="Wang L" first="Lun" last="Wang">Lun Wang</name>
<name sortKey="Wu, Xiao Meng" sort="Wu, Xiao Meng" uniqKey="Wu X" first="Xiao-Meng" last="Wu">Xiao-Meng Wu</name>
<name sortKey="Xu, Qiang" sort="Xu, Qiang" uniqKey="Xu Q" first="Qiang" last="Xu">Qiang Xu</name>
<name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name>
<name sortKey="Zheng, Bei Bei" sort="Zheng, Bei Bei" uniqKey="Zheng B" first="Bei-Bei" last="Zheng">Bei-Bei Zheng</name>
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</tree>
</affiliations>
</record>

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