Gene expression analysis revealed Hbr-miR396b as a key piece participating in reaction wood formation of Hevea brasiliensis (rubber tree)

Meng, Xiangxu; Kong, Lingshan; Zhang, Yuanyuan; Wu, Mengjia; Wang, Yue; Li, Jia; Jiao, Nanbo; Xu, Jiahong; Chen, Jinhui; Tu, Zhihua

doi:10.1016/j.indcrop.2021.114460

Cited by 5 publications

(6 citation statements)

References 65 publications

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“…MiRNAs are an important class of non-coding factors that regulate genes expression at the post-transcriptional level in nearly every aspect of plant development such as germination, growth, tissue differentiation, and flowering ( Das et al, 2019 ; Glazińska et al, 2019 ; Qiu et al, 2019 ). The results of small RNA-seq demonstrate that the xylem of D. odorifera contains a large and diverse small RNA population, a finding similar to previous studies in rubber tree ( Meng et al, 2022 ) and Chinese fir ( Wan et al, 2012 ).…”

Section: Discussionsupporting

confidence: 87%

“…A total of 40 known miRNAs belonging to 22 miRNA families and 123 novel miRNAs were identified in these small RNA libraries, among which 14 miRNAs were differentially expressed ( Figure 4 ). Similarly, the miR156, miR159, miR166, miR319, miR396, miR398, and miR408 families have also been identified in the xylem of rubber tree ( Meng et al, 2022 ). The miR396a and miR156g are also differentially expressed in the primary stem, transition stem, and secondary stem of Populus trichocarpa ( Wang R et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

“…We used the miRNA RT-qPCR Detection Kit (Aidlab, Beijing, China) for RT-qPCR analysis of miRNAs, following the manufacturer’s recommendations. PCR amplification was performed at a preheated (94°C) thermal cycler and samples were incubated at 94 °C for 2 min, followed by 40 cycles of 94°C for 15 s and 60°C for 40 s. The U6 gene served as an internal control for normalization ( Meng et al, 2022 ). The 2 –△△Ct method was used to calculate the expression levels of the miRNAs and genes against the internal controls ( Schmittgen and Livak, 2008 ).…”

Section: Methodsmentioning

confidence: 99%

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Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Zhao

Meng

et al. 2022

Front. Genet.

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Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms “amino acid binding,” “cellulase activity,” and “DNA beta-glucosyltransferase activity”. Further, KEGG pathway annotation showed significant enrichment in “fatty acid elongation” and “biosynthesis of unsaturated fatty acids”. These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Zhao

Meng

et al. 2022

Front. Genet.

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“…qPCR was performed with TB Green Premix Ex Taq II (Tli RNase H Plus; Takara, Beijing, China) for the target genes according to the manufacturer’s instructions. PCR conditions were as follows: denaturation at 94°C for 2 min, then 40 cycles of 95°C for 5 s and 60°C for 30 s. Ubiquitin was used as internal reference for normalization of expression data of rubber tree samples ( Meng et al., 2022 ), and β-actin was used for N. benthamiana ( Nawaz et al., 2019 ). For miRNA, a miRNA RT-qPCR Detection Kit (Aidlab, Beijing, China) was used following the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

Multiomics studies with co-transformation reveal microRNAs via miRNA-TF-mRNA network participating in wood formation in Hevea brasiliensis

Chen,

Liu,

Meng

et al. 2023

Front. Plant Sci.

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IntroductionMicroRNAs (miRNAs) are small endogenous non-coding RNAs that play an important role in wood formation in plants. However, the significance of the link between miRNAs and their target transcripts in wood formation remains unclear in rubber tree (Hevea brasiliensis).MethodsIn this study, we induced the formation of reaction wood by artificially bending rubber trees for 300 days and performed small RNA sequencing and transcriptome deep sequencing (RNA-seq) to describe the complement of miRNAs and their targets contributing to this process.Results and discussionWe identified 5, 11, and 2 differentially abundant miRNAs in normal wood (NW) compared to tension wood (TW), in NW relative to opposite wood (OW), and between TW and OW, respectively. We also identified 12 novel miRNAs and 39 potential miRNA-mRNA pairs with different accumulation patterns in NW, TW, and OW. We noticed that many miRNAs targeted transcription factor genes, which were enriched in KEGG pathways associated with phenylpropanoid biosynthesis, phenylalanine metabolism, and pyruvate metabolism. Thus, miRNA-TF-mRNA network involved in wood formation via tension wood model were constructed. We validated the differential accumulation of miRNAs and their targets by RT-qPCR analysis and overexpressed miRNA in Nicotiana benthamiana with its potential target gene. These results will provide a reference for a deep exploration of growth and development in rubber tree.

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“…qPCR was performed with TB Green Premix Ex Taq II (Tli RNase H Plus; Takara, Beijing, China) for the target genes according to the manufacturer's instructions. PCR conditions were as follows: denaturation at 94°C for 2 min, then 40 cycles of 95°C for 5 s and 60°C for 30 s. Ubiquitin was used as internal reference for normalization of expression data of rubber tree samples (Meng et al, 2022), and b-actin was used for N. benthamiana (Nawaz et al, 2019). For miRNA, a miRNA RT-qPCR Detection Kit (Aidlab, Beijing, China) was used following the manufacturer's instructions.…”

Section: Validation Of Mirna Expression and That Of Their Target Gene...mentioning

confidence: 99%

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

2024

Frontiers Research Topics

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Gene expression analysis revealed Hbr-miR396b as a key piece participating in reaction wood formation of Hevea brasiliensis (rubber tree)

Cited by 5 publications

References 65 publications

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Multiomics studies with co-transformation reveal microRNAs via miRNA-TF-mRNA network participating in wood formation in Hevea brasiliensis

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

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