Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis

Kanjanawattanawong, Supanath; Tangphatsornruang, Sithichoke; Triwitayakorn, Kanokporn; Ruang-areerate, Panthita; Sangsrakru, Duangjai; Poopear, Supannee; Somyong, Suthasinee; Narangajavana, Jarunya

doi:10.1007/s00438-014-0862-0

Cited by 14 publications

(11 citation statements)

References 47 publications

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“…Available data sets from five small-RNA-seq data were generated by (Gébelin et al, 2012;Gébelin et al, 2013b;Kanjanawattanawong et al, 2014;Lertpanyasampatha et al, 2012) comprising juvenile plants, latex of healthy and TPD-affected trees, young and fully developed leaves from mature trees. Complete tissue-specific (embryo, flower, latex, leaf, bark, root) transcriptomes were generated by Duan et al (2013) and Piyatrakul et al (2012).…”

Section: Plant Materials and Rna Samplesmentioning

confidence: 99%

“…MITP (https://sourceforge. net/projects/mitp/) was chosen with default parameters to identify hairpin structures and miRNAs in available small RNA datasets (Gébelin et al, 2012;Gébelin et al, 2013b;Kanjanawattanawong et al, 2014;Lertpanyasampatha et al, 2012). The small RNA-seq data described in Gébelin et al are available under project number PRJCA001333 in the GSA (Wang et al, 2017a) and BIG Data Center (BIG Data Center Members, 2018).…”

Section: Mir Gene Identificationmentioning

confidence: 99%

“…This observation led to the need to annotate small RNAs to decipher their biological activity, in particular that of 20-22 nt (miRNA and ta-siRNA). Although not complete, previous studies characterised endogenous miRNAs in Hevea, thereby enabling the identification of 68 and 16 species-specific families, thanks to the availability of a reference transcriptome from clone PB 260 (Gébelin et al, 2012;Gébelin et al, 2013b;Kanjanawattanawong et al, 2014;Lertpanyasampatha et al, 2012). The aim of the present study was to complete the annotation of Hevea microRNAs and ta-siRNAs thanks to the availability of genomic sequences from clone PB 260 (Zhang et al, 2019).…”

Section: Introductionmentioning

confidence: 97%

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Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Leclercq

Farinas

et al. 2020

PeerJ

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Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.

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Section: Plant Materials and Rna Samplesmentioning

confidence: 99%

Section: Mir Gene Identificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Leclercq

Farinas

et al. 2020

PeerJ

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“…MicroRNAs (miRNAs) have attracted much attention for their various roles in post-transcriptional regulation of protein coding genes and their importance in many different pathways [ 21 , 22 ], such as in the development of roots [ 23 – 26 ], shoots [ 27 , 28 ], leaves [ 29 – 31 ] and flowers [ 32 – 34 ], as well as cell fate [ 35 , 36 ]. Additionally, they were also found to play roles in responses to phytohormones [ 37 , 38 ], nutrients [ 39 – 42 ], and environmental stresses [ 43 – 47 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L.

Liu

Gao

et al. 2016

PLoS ONE

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The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.

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“…While many data exist about the P. infestans and P. sojae genome, those related to P. cinnamomi are scanty. Genomic DNA libraries are a standard procedure which has been used to sequencing genes in several organisms (Kanjanawattanawong et al, 2014;Tan et al, 2014). By digestion of genomic DNA from P. cinnamomi we have constructed a DNA library with an insert size average of 2-12 kb in Escherichia coli.…”

Section: Introductionmentioning

confidence: 99%

Genes found in partial sequencing of Phytophthora cinnamomi genome

Santos¹,

Martins²,

Maia³

et al. 2016

Rev. Ciênc. Agr.

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A B S T R A C TMembers of the oomycete cause extensive losses in agriculture and widespread degradation in natural plant communities, being responsible for the death of thousands of trees every year. Two of the representative species are Phytophthora infestans, which causes late blight of potato, and Phytophthora cinnamomi, which causes chestnut ink disease, responsible for losses on sweet chestnut production in Europe. Genome sequencing efforts have been focused on the study of three species: P. infestans, P. sojae and P. ramorum. Phytophthora infestans has been developed as the model specie for the genus, possessing excellent genetic and genomics resources including genetic maps, BAC libraries, and EST sequences. Our research team is trying to sequence the genome of P. cinnamomi in order to gain a better understanding of this oomycete, to study changes in plant-pathogen relationships including those resulting from climate change and trying to decrease the pathogen's impact on crops and plants in natural ecosystems worldwide. We present here a preliminary report of partially sequenced genomic DNA from P. cinnamomi encoding putative protein-coding sequences and tRNAs. Database analysis reveals the presence of genes conserved in oomycetes.Keywords: DNA library, oomycetes, Phytophthora cinnamomi, tRNA. R E S U M OOs oomicetas causam enormes perdas na agricultura e degradação generalizada em áreas de crescimento natural, sendo responsáveis pela morte de milhares de árvores por ano. Duas das espécies representativas de oomicetas são Phytophthora infestans, que provoca o míldio da batateira, e Phytophthora cinnamomi, que causa a doença da tinta do castanheiro, responsável por perdas de produção de castanha na Europa. Os esforços de sequenciação de genomas de oomicetas têm estado focados no estudo de três espécies: P. infestans, P. sojae e P. ramorum. Phytophthora infestans foi considerada como espécie modelo para o género, pois possui excelentes recursos genéticos e de genómica, incluindo mapas genéticos, bibliotecas BAC, e sequências de EST. Esta equipa de investigadores procura sequenciar o genoma de P. cinnamomi, a fim de obter uma melhor compreensão deste oomiceta, para estudar mudanças nas relações plantapatogénio, incluindo as resultantes das alterações climáticas, e tentando diminuir o impacto do patogénio nas culturas e plantas em ecossistemas naturais em todo o mundo. É apresentada uma abordagem preliminar do DNA genómico parcialmente sequenciado a partir de P. cinnamomi, o qual codifica possíveis sequências de proteínas e tRNAs. As análises em bases de dados revelam a presença de genes conservados em oomicetas.Palavras-chave: Biblioteca DNA, oomicetas, Phytophthora cinnamomi, tRNA.

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Characterization of rubber tree microRNA in phytohormone response using large genomic DNA libraries, promoter sequence and gene expression analysis

Cited by 14 publications

References 47 publications

Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L.

Genes found in partial sequencing of Phytophthora cinnamomi genome

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