Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing

MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species

Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)

Crofton weed (Ageratina adenophora) is one of the most hazardous invasive plant species, which causes serious economic losses and environmental damages worldwide. However, the sequence resource and genome information of A. adenophora are rather limited, making phylogenetic identification and evolutionary studies very difficult. Here, we report the complete sequence of the A. adenophora chloroplast (cp) genome based on Illumina sequencing.The A. adenophora cp genome is 150, 689 bp in length including a small single-copy (SSC) region of 18, 358 bp and a large single-copy (LSC) region of 84, 815 bp separated by a pair of inverted repeats (IRs) of 23, 755 bp. The genome contains 130 unique genes and 18 duplicated in the IR regions, with the gene content and organization similar to other Asteraceae cp genomes. Comparative analysis identified five DNA regions (ndhD-ccsA, psbI-trnS, ndhF-ycf1, ndhI-ndhG and atpA-trnR) containing parsimony-informative characters higher than 2%, which may be potential informative markers for barcoding and phylogenetic analysis. Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution. Phylogenetic analysis demonstrated a sister relationship between A. adenophora and Guizotia abyssinica and supported a monophyly of the Asterales.We have assembled and analyzed the chloroplast genome of A. adenophora in this study, which was the first sequenced plastome in the Eupatorieae tribe. The complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies within this invasive species and also within the Asteraceae family

Comparative Analysis of the Transcriptional Response of Tolerant and Sensitive Wheat Genotypes to Drought Stress in Field Conditions

Drought stress is one of the most adverse environmental limiting factors for wheat (Triticum aestivum L.) productivity worldwide. For better understanding of the molecular mechanism of wheat in response to drought, a comparative transcriptome approach was applied to investigate the gene expression change of two wheat cultivars, Jimai No. 47 (drought-tolerant) and Yanzhan No. 4110 (drought-sensitive) in the field under irrigated and drought-stressed conditions. A total of 3754 and 2325 differential expressed genes (DEGs) were found in Jimai No. 47 and Yanzhan No. 4110, respectively, of which 377 genes were overlapped, which could be considered to be the potential drought-responsive genes. GO (Gene Ontology) analysis showed that these DEGs of tolerant genotype were significantly enriched in signaling transduction and MAP (mitogen-activated protein) kinase activity, while that of sensitive genotype was involved in photosynthesis, membrane protein complex, and guard cell differentiation. Furthermore, 32 and 2 RNA editing sites were identified in drought-tolerant and sensitive genotypes under drought compared to irrigation, demonstrating that RNA editing also plays an important role in response to drought in wheat. This study investigated the gene expression pattern and RNA editing sites of two wheat cultivars with contrasting tolerance in field condition, which will contribute to a better understanding of the molecular mechanism of drought tolerance in wheat and beyond

Percent identity plot for comparison of six Asteraceae chloroplast genomes using mVISTA program.

<p>Top line shows genes in order (transcriptional direction indicated with arrow). Sequence similarity of aligned regions between <i>A. adenophora</i> and other five species is shown as horizontal bars indicating average percent identity between 50–100% (shown on y-axis of graph). The x-axis represents the coordinate in the chloroplast genome. Genome regions are color coded as protein-coding (exon), rRNA, tRNA and conserved non-coding sequences (CNS).</p

The genes having intron in the <i>A. adenophora</i> cp genome and the length of the exons and introns.

*<p>rps12 is trans-spliced gene with 5′ end exon located in the LSC region and the duplicated 3′ end exon located in IR regions.</p

Promising regions identified for developing phylogenetic markers in Asteraceae family.

*<p>commonly used phylogenetic markers included for comparison.</p

Maximum parsimony (MP) trees of all the selected 24 chloroplast regions of six Asteraceae species

<p>. The phylogram of “combined regions” was constructed from the MP analysis using all the 24 regions together.</p

The MP phylogenetic tree is based on 35 protein-coding genes from 33

<p> <b>plant taxa.</b> The MP tree has a length of 41, 661 with a consistency index of 0.4644 and a retention index of 0.6821. Numbers above node are bootstrap support values. ML tree has the same topology but is not shown.</p

Repeat structure analysis in the <i>A. adenophora</i> cp genome.

<p>The cutoff value for tandem repeat is 15 bp and 30 bp for dispersed repeat. A. Frequency of repeats by length; B. Repeat type; C. Location distribution of all the repeats.</p

The codon–anticodon recognition pattern and codon usage for <i>A. adenophora</i> cp genome.

*<p>Numerals indicate the frequency of usage of each codon in 24894 codons in 87 potential protein-coding genes.</p