Histogram of GO classifications of assembled Chinese jujube (<i>Ziziphus jujuba M.</i>) unigenes.

<p>Results are summarized for three main GO categories: biological process, cellular component and molecular function.</p

Summary of transcriptome sequencing of Chinese jujube fruit using 454 GS FLX Titanium.

<p>Summary of transcriptome sequencing of Chinese jujube fruit using 454 GS FLX Titanium.</p

<i>De Novo</i> Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

<div><p>Chinese jujube (<i>Ziziphus jujuba</i> Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then <i>de novo</i> assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and <i>Z. mauritiana Lam</i> and <i>Z. acidojujuba</i> as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in <i>Z. jujuba</i>. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.</p></div

Up-regulated and down-regulated UniGenes expression profiles during Chinese jujube fruit development presented by GO classification.

<p>Up-regulated and down-regulated UniGenes expression profiles during Chinese jujube fruit development presented by GO classification.</p

Summary of identifying SSR loci from the unigenes of Chinese jujube.

<p>Summary of identifying SSR loci from the unigenes of Chinese jujube.</p

Distribution of different repeat type classes in fruit transcriptome of Chinese jujube.

<p>Distribution of different repeat type classes in fruit transcriptome of Chinese jujube.</p

Frequency of classified novel developed SSR repeat types.

<p>Frequency of classified novel developed SSR repeat types.</p

Silver stained polyacrylamide gels of four example SSR loci showed microsatellite polymorphisms in Chinese jujube and related species.

<p>The SSR loci BFU2038, BFU2113, BFU2134 and BFU2143 are corresponding to A, B, C and D, respectively. Lane1, ‘Hupingzao’; Lane2, ‘Yuanling’; Lane3, ‘Dongzao’; Lane4, ‘Junzao’; Lane5, ‘Jidanzao’; Lane6, ‘Mayizao’; Lane7, ‘Jinsixiaozao’; Lane8, ‘Huizao’; Lane9, ‘Anonymous’; Lane10, ‘Wanglang’.</p

Graphical visualization of significantly differentially expressed genes versus transcripts as designed by the RSEM software.

<p>The <i>y</i>-axis indicates differences in the logarithms between the expression of the ‘g’ gene of the sample K, K ', while the <i>x</i>-axis indicates the average of the logarithm for the expression of the ‘g’ gene of the sample K, K '. log CPM: the average log2-counts-per-million.</p

List of the <i>Ziziphus</i> accessions used in this study.

<p>List of the <i>Ziziphus</i> accessions used in this study.</p