Junior Recital

List of performers and performances

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

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

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

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

Transcriptome Analysis by Illumina High-Throughout Paired-End Sequencing Reveals the Complexity of Differential Gene Expression during <i>In Vitro</i> Plantlet Growth and Flowering in <i>Amaranthus tricolor</i> L.

<div><p><i>Amaranthus tricolor</i> L. is a C₄ plant, which is consumed as a major leafy vegetable in some tropical countries. Under conditions of high temperature and short daylight, <i>Am. tricolor</i> readily bolts and blooms, degrading leaf quality. A preliminary <i>in vitro</i> flowering study demonstrated that the flowering control pathway in <i>Am. tricolor</i> may differ from that of <i>Arabidopsis</i>. Nevertheless, no transcriptome analysis of the flowering process in <i>Amaranthus</i> has been conducted. To study <i>Am. tricolor</i> floral regulatory mechanisms, we conducted a large-scale transcriptome analysis—based on Illumina HiSeq sequencing of cDNA libraries generated from <i>Am. tricolor</i> at young seedling (YSS), adult seedling (ASS), flower bud (FBS), and flowering (FS) stages. A total of 99,312 unigenes were obtained. Using BLASTX, 43,088 unigenes (43.39%) were found to have significant similarity with accessions in Nr, Nt, and Swiss-Prot databases. Of these unigenes, 11,291 were mapped to 266 KEGG pathways. Further analysis of the four digital transcriptomes revealed that 735, 17,184, 274, and 206 unigenes were specifically expressed during YSS, ASS, FBS, and FS, respectively, with 59,517 unigenes expressed throughout the four stages. These unigenes were involved in many metabolic pathways related to <i>in vitro</i> flowering. Among these pathways, 259 unigenes were associated with ubiquitin-mediated proteolysis, indicating its importance for <i>in vitro</i> flowering in <i>Am. tricolor</i>. Other pathways, such as circadian rhythm and cell cycle, also had important roles. Finally, 26 unigenes were validated by qRT-PCR in samples from <i>Am. tricolor</i> at YSS, ASS, FBS, and FS; their differential expressions at the various stages indicate their possible roles in <i>Am. tricolor</i> growth and development, but the results were somewhat similar to <i>Arabidopsis</i>. Because unigenes involved in many metabolic pathways or of unknown function were revealed to regulate <i>in vitro</i> plantlet growth and flowering in <i>Am. tricolor</i>, the process appears to be highly complex in this species.</p></div

Summary of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.

<p>Summary of unigenes generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.</p

Results of qRT-PCR analysis of 26 candidate unigenes during <i>Am. tricolor in vitro</i> plantlet growth and flowering.

<p>(a) Plant circadian rhythm pathway-related unigenes. (b) Ubiquitin-mediated proteolysis pathway-related unigenes. (c–d) Genes related to other or unknown pathways.</p

Statistical summary of reads generated by transcriptome sequencing of <i>in vitro</i> plantlets of <i>Am. tricolor</i>.

1<p>YSS  =  young seedling stage; ASS  =  adult seedling stage; FBS  =  flower bud stage; FS  =  flowering stage.</p