Additional file 2: Figure S1. of The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes

Length distribution of small RNA sequences in two libraries obtained from durum wheat Ciccio and Svevo cultivars. (DOCX 15 kb

Additional file 1: Table S1. of The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes

List of primers used for Q-RT-PCR assay for durum wheat miRNAs and their putative target genes. (XLSX 14 kb

Additional file 3: Table S2. of The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes

Conserved miRNAs identified in durum wheat Ciccio and Svevo cultivars by Illumina sequencing. MiRNAs were annotated according to miRBase release 21. (XLSX 16 kb

Cynara MSA for phylogeny

Cynara MSA for phylogen

Additional file 4: Table S3. of The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes

Novel miRNAs from durum wheat identified in durum wheat Ciccio and Svevo cultivars by Illumina sequencing. MiRNAs were predicted in silico using similarity search and secondary structure analyses of putative pre-miRNAs sequences. (XLSX 51 kb

Cynara MSA

Cynara MS

Cynara maximum parsimony tree

Cynara maximum parsimony tre

Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae

<div><p>With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the <i>ndhF</i> gene generating an overlap between the <i>ndhF</i> and <i>ycf1</i> genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the <i>Cynara</i> genus. Parsimony-informative regions were evaluated and allowed to place a <i>Cynara</i> species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for “specific barcode” purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.</p></div

Phylogenetic tree based on maximum parsimony of 69 accessions belonging to the Asteraceae family.

<p>Seven coding regions were used: <i>matk</i>, <i>ndhD</i>, <i>ndhF</i>, <i>ndhI</i>, <i>rbcL</i>, <i>rpoB</i> and the first exon of <i>rpoC1</i>, for a total of 1,811 parsimony-informative characters. Sequences from <i>C</i>. <i>cardunculus</i> were obtained from this work. Bootstrap values for each node were set greater than 50%. Species for which the complete cp genome is available are shaded.</p

Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage

<div><p>Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation. A number of target genes were predicted to be involved in nitrogen metabolism. An inverse correlation for the qPCR expression data of miRNA/target pairs miR399b/<i>PHO2</i>, miR393c/<i>AFB2</i>, ttu-novel-61/<i>CCAAT-TF</i> was observed in specific tissues or cultivar. Especially, ttu-novel-61 was down-regulated and its target <i>CCAAT-TF</i> up-regulated in almost all tissues both in Svevo and in Ciccio. Moreover, <i>CCAAT-TF</i> was confirmed to be cleaved by ttu-novel-61 at the expected site. The discovery of miRNAs involved in the response to nitrogen stress represents an important step towards functional analyses, with the final aim to design strategies for improving nitrogen use efficiency in durum wheat.</p></div