KOG function classification of the genes expressed specifically or preferentially in the selfed ovules of <i>Xanthoceras sorbifolium</i>.

<p>The X-axis indicates KOG function classification. The Y-axis indicates number of unigenes.</p

The overrepresented functional GO terms of the genes specifically or preferentially in the selfed ovules of <i>Xanthoceras sorbifolium</i>.

<p>The overrepresented functional GO terms of the genes specifically or preferentially in the selfed ovules of <i>Xanthoceras sorbifolium</i>.</p

Comparative <i>De Novo</i> Transcriptome Analysis of Fertilized Ovules in <i>Xanthoceras sorbifolium</i> Uncovered a Pool of Genes Expressed Specifically or Preferentially in the Selfed Ovule That Are Potentially Involved in Late-Acting Self-Incompatibility

<div><p><i>Xanthoceras sorbifolium</i>, a tree species endemic to northern China, has high oil content in its seeds and is recognized as an important biodiesel crop. The plant is characterized by late-acting self-incompatibility (LSI). LSI was found to occur in many angiosperm species and plays an important role in reducing inbreeding and its harmful effects, as do gametophytic self-incompatibility (GSI) and sporophytic self-incompatibility (SSI). Molecular mechanisms of conventional GSI and SSI have been well characterized in several families, but no effort has been made to identify the genes involved in the LSI process. The present studies indicated that there were no significant differences in structural and histological features between the self- and cross-pollinated ovules during the early stages of ovule development until 5 days after pollination (DAP). This suggests that 5 DAP is likely to be a turning point for the development of the selfed ovules. Comparative <i>de novo</i> transcriptome analysis of the selfed and crossed ovules at 5 DAP identified 274 genes expressed specifically or preferentially in the selfed ovules. These genes contained a significant proportion of genes predicted to function in the biosynthesis of secondary metabolites, consistent with our histological observations in the fertilized ovules. The genes encoding signal transduction-related components, such as protein kinases and protein phosphatases, are overrepresented in the selfed ovules. <i>X</i>. <i>sorbifolium</i> selfed ovules also specifically or preferentially express many unique transcription factor (TF) genes that could potentially be involved in the novel mechanisms of LSI. We also identified 42 genes significantly up-regulated in the crossed ovules compared to the selfed ovules. The expression of all 16 genes selected from the RNA-seq data was validated using PCR in the selfed and crossed ovules. This study represents the first genome-wide identification of genes expressed in the fertilized ovules of an LSI species. The availability of a pool of specifically or preferentially expressed genes from selfed ovules for <i>X</i>. <i>sorbifolium</i> will be a valuable resource for future genetic analyses of candidate genes involved in the LSI response.</p></div

Top 25 transcription factor families of the <i>Xanthoceras sorbifolium</i> selfed ovule dataset.

<p>The X-axis indicates the top 25 TF families. The Y-axis indicates the number of unigenes assigned to a specific TF family.</p

Gene Ontology categories of assembled unigenes.

<p>Unigenes were assigned to three main categories (biological processes, cellular components, and molecular functions) and 51 subcategories. The X-axis indicates GO term. The Y-axis indicates number of unigenes.</p

The <i>Xanthoceras sorbifolium</i> selfed ovule specifically or preferentially expressed genes were annotated to BRITE functional hierarchies.

<p>The <i>Xanthoceras sorbifolium</i> selfed ovule specifically or preferentially expressed genes were annotated to BRITE functional hierarchies.</p

GO function classification of the identified genes expressed specifically or preferentially in the crossed ovules of <i>Xanthoceras sorbifolium</i>.

<p>GO function classification of the identified genes expressed specifically or preferentially in the crossed ovules of <i>Xanthoceras sorbifolium</i>.</p

Twenty-eight specifically or preferentially expressed unigenes in the selfed ovules of <i>Xanthoceras sorbifolium</i> encode for the putative transcription factors belonging to 12 different families.

<p>RPKM: Reads per Kilobase per Million reads.</p

Mean area of the median longitudinal section of ovule and embryo sac after cross- and self- pollination of <i>Xanthoceras sorbifolium</i>.

<p>A: Ovule area; B: Embryo sac area.</p

The selfed and crossed ovules were harvested from the pistil at 5 d after pollination for the study of RNA-seq and morphology.

<p>A and B showing the crossed and selfed ovules (arrows), respectively.</p