IMB 1800 Programs for Data processing at the Accelerators of the Central Bureau for Nuclear Measurements. Part 3: Programs for Interactive Data Reduction. EUR 4404.

<p>A, miR393 and <i>DlCHS</i>; B, miR393 and <i>DlCHI</i>; C, miR393 and <i>DlFLS</i>; D, miR393 and <i>DlF3′H</i>; E, miR393 and <i>DlDFR</i>; F, miR393 and <i>DlLAR</i>; G, miR393 and its target gene <i>DlTIR1-3</i>.</p

qPCR analysis of relative expressions of known and novel miRNAs, 5S rRNA, and U6 snRNA during longan SE.

<p>The bar represents the scale of relative expression levels of miRNAs, and colors indicate relative signal intensities of miRNAs. Each column represents a sample, and each row represents a single miRNA. Samples: 1. friable-embryogenic callus(EC); 2. embryogenic callus II(EC II); 3. incomplete compact pro-embryogenic cultures(ICpEC); 4. compact pro-embryogenic cultures(CpEC); 5. globular embryos(GE); 6. heart-shaped embryos(HE); 7. torpedo- shaped embryos(TE); 8. cotyledonary embryos(CE); 9. mature embryos(ME).</p

Comparative Analysis Reveals Dynamic Changes in miRNAs and Their Targets and Expression during Somatic Embryogenesis in Longan (<i>Dimocarpus longan</i> Lour.)

<div><p>Somatic embryogenesis (SE), which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs) are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (<i>Dimocarpus longan</i>) SE. A total of 643 conserved and 29 novel miRNAs (including star strands) from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were <i>dlo-miR156</i> family members and <i>dlo-miR166c*</i> associated with early embryonic culture developmental stages; <i>dlo-miR26</i>, <i>dlo-miR160a</i>, and families <i>dlo-miR159</i>, <i>dlo-miR390,</i> and <i>dlo-miR398b</i> related to heart-shaped and torpedo- shaped embryo formation; <i>dlo-miR4a, dlo-miR24, dlo-miR167a</i>, <i>dlo-miR168a*</i>, <i>dlo-miR397a</i>, <i>dlo-miR398b.1</i>, <i>dlo-miR398b.2</i>, <i>dlo-miR808</i> and <i>dlo-miR5077</i> involved in cotyledonary embryonic development; and <i>dlo-miR17</i> and <i>dlo-miR2089*-1</i> that have regulatory roles during longan SE. In addition, <i>dlo-miR167a</i>, <i>dlo-miR808</i>, and <i>dlo-miR5077</i> may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and provide insights into miRNA biogenesis and expression in plant somatic embryo development.</p></div

Distribution of small RNAs among different categories in <i>Dimocarpus longan.</i>

<p>Distribution of small RNAs among different categories in <i>Dimocarpus longan.</i></p

Longan-specific miRNAs identified from <i>Dimocarpus longan</i> transcriptome and populus genome.

<p>Longan-specific miRNAs identified from <i>Dimocarpus longan</i> transcriptome and populus genome.</p

Validation of DEGs by qPCR (comparing with FPKM values) during cold stress in the wild banana showing the FPKM data confirmed by qPCR tests.

<p>Validation of DEGs by qPCR (comparing with FPKM values) during cold stress in the wild banana showing the FPKM data confirmed by qPCR tests.</p

Critical plays: An exploration in truth and verisimilitude

[No abstract available

Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (<i>Musa itinerans</i>)

<div><p>Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana.</p></div

Genome-wide identification and characterization of the <i>CKII</i> gene family in the cultivated banana cultivar (<i>Musa</i> spp. cv Tianbaojiao) and the wild banana (<i>Musa itinerans</i>)

<div><p>Plant casein kinase II (CKII) plays an essential role in regulating plant growth and development, and responses to biotic and abiotic stresses. Here, we report the identification and characterization of the <i>CKII</i> family genes in <i>Musa</i> spp. cv. ‘Tianbaojiao’ (AAA group) and the wild banana (<i>Musa itinerans</i>). The 13 cDNA sequences of the <i>CKII</i> family members were identified both in ‘Tianbaojiao’ and wild banana, respectively. The differences between <i>CKII</i> α and <i>CKII</i> β members are corroborated through the subcellular localizations, phosphorylation sites and gene structures. The cloning of <i>CKII β-like-2</i> gDNA sequences in wild banana and ‘Tianbaojiao’ and the analysis of gene structures showed <i>MiCKIIβ-like-2b</i> and <i>MaCKIIβ-like-2</i> are likely alternatively spliced transcripts, which were derived from the alternative splicing events that involved exon deletion. The qPCR validation showed differential expression <i>CKII</i> family members in response to cold stress and also in all tested tissues (leaf, pseudostem and root) of wild banana. In particular, the normal transcript <i>MiCKIIβ-like-2a</i> was highly expressed in response to cold stress in wild banana; oppositely, the alternatively spliced transcript <i>MiCKIIβ-like-2b</i> was quite lowly expressed. The complex origin and long-term evolution of <i>Musa</i> lineage might explain the alternative splicing events of <i>CKII β-like-2</i>.</p></div

Combined small RNA and degradome sequencing reveals complex microRNA regulation of catechin biosynthesis in tea (<i>Camellia sinensis</i>)

<div><p>MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5’cDNA ends (RLM-RACE) were applied. Using degradome sequencing, 26 genes mainly involved in transcription factor, resistance protein and signal transduction protein synthesis were identified as potential miRNA targets, with 5 genes subsequently verified. Quantitative real-time PCR (qRT-PCR) revealed that the expression patterns of novel-miR1, novel-miR2, csn-miR160a, csn-miR162a, csn-miR394 and csn-miR396a were negatively correlated with catechin content. The expression of six miRNAs (csn-miRNA167a, csn-miR2593e, csn-miR4380a, csn-miR3444b, csn-miR5251 and csn-miR7777-5p.1) and their target genes involved in catechin biosynthesis were also analyzed by qRT-PCR. Negative and positive correlations were found between these miRNAs and catechin contents, while positive correlations were found between their target genes and catechin content. This result suggests that these miRNAs may negatively regulate catechin biosynthesis by down-regulating their biosynthesis-related target genes. Taken together, our results indicate that miRNAs are crucial regulators in tea, with the results of 5’-RLM-RACE and expression analyses revealing the important role of miRNAs in catechin anabolism. Our findings should facilitate future research to elucidate the function of miRNAs in catechin biosynthesis.</p></div