Gene ontology classes.

<p>Percentage of differentially expressed contigs annotated for Biological Process, Cellular Component and Molecular Function GO categories. *indicates a significant estimation at 0.05.</p

Distribution of log₂ fold change for differentially expressed genes.

<p>A and B are distribution of log₂ FC in anther and ovary, respectively.</p

The list of primers used for gene expression analysis by quantitative Real Time PCR.

<p>Corresponding annealing temperatures and amplicon sizes are shown for each gene.</p><p>Abbreviations: F, Forward primer; R, Reverse primer.</p

Homology of almond transcriptome to other plant species.

<p>The percent of BLASTX top-hit with different plant species. Maximum homology of almond transcripts were observed with peach (<i>Prunus persica</i>).</p

Statistics of <i>de</i><i>novo</i> transcriptome assembly and annotation.

<p><i>De novo</i> assembley was performed using Trinity package following the standard manual. Annotation was achieved using BLASTX program. Mapping statistics of reads to the transcriptome assemblies and peach genome are also provided, which was obtained using Bowtie v2 package.</p><p>Abbreviations: HSA, stressed anther of H genotype; HCA, control anther of H genotype; HSO, stressed ovary of H genotype; HCO, control ovary of H genotype.</p

Distribution of differentially expressed genes of almond under frost stress.

<p>Venn diagram indicating the number of differentially expressed contigs under frost in anther and ovary tissues of almond.</p

Basic statistics of RNA-seq reads in almond obtained from Illumina HiSeq-2000.

<p>The qualtiy of reads in Fastq files were analyzed using FastQC software. The reads were subjected to vigorous quality filtering using FastX toolkit before further analysis.</p><p>Abbreviations: HSA, stressed anther of H genotype; HCA, control anther of H genotype; HSO, stressed ovary of H genotype; HCO, control ovary of H genotype.</p

Our pipeline for RNA-seq analysis in almond under control and frost stress conditions.

<p>Two almond tissues (anther and ovary) were subjected to untreated and −2°C conditions. Following the RNA exteraction, cDNA library was constructed and sequencing was performed using an IIlumina platform. <i>De novo</i> transcript assembly was conducted after quality control and trimming the reads and then contigs were annotated. Transcript aboundance and differentially expressed genes were analyzed using RSEM and EBseq, respectively. Finally, gene ontology were determined for each set of genes in the DE list.</p

A side view of almond flowers used in this study.

<p>The popcorn stage of almond flower showed in A. The position of anther and ovary tissues in almond which were collected for the RNA-seq analysis showed in B.</p