BackgroundYellow horn (Xanthoceras sorbifolia Bunge) is an oil-rich seed shrub that grows well in cold, barren environments and has great potential for biodiesel production in China. However, the limited genetic data means that little information about the key genes involved in oil biosynthesis is available, which limits further improvement of this species. In this study, we describe sequencing and de novo transcriptome assembly to produce the first comprehensive and integrated genomic resource for yellow horn and identify the pathways and key genes related to oil accumulation. In addition, potential molecular markers were identified and compiled.Methodology/Principal FindingsTotal RNA was isolated from 30 plants from two regions, including buds, leaves, flowers and seeds. Equal quantities of RNA from these tissues were pooled to construct a cDNA library for 454 pyrosequencing. A total of 1,147,624 high-quality reads with total and average lengths of 530.6 Mb and 462 bp, respectively, were generated. These reads were assembled into 51,867 unigenes, corresponding to a total of 36.1 Mb with a mean length, N50 and median of 696, 928 and 570 bp, respectively. Of the unigenes, 17,541 (33.82%) were unmatched in any public protein databases. We identified 281 unigenes that may be involved in de novo fatty acid (FA) and triacylglycerol (TAG) biosynthesis and metabolism. Furthermore, 6,707 SSRs, 16,925 SNPs and 6,201 InDels with high-confidence were also identified in this study.ConclusionsThis transcriptome represents a new functional genomics resource and a foundation for further studies on the metabolic engineering of yellow horn to increase oil content and modify oil composition. The potential molecular markers identified in this study provide a basis for polymorphism analysis of Xanthoceras, and even Sapindaceae; they will also accelerate the process of breeding new varieties with better agronomic characteristics.

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Research Highlights: The critical period of sex differentiation in Xanthoceras sorbifolium was investigated. Multiple microRNAs (miRNAs) were identified to influence female and male flower development, with some complementary functions. Background and Objectives: Xanthoceras sorbifolium Bunge is widely cultivated owing to its multipurpose usefulness. However, as a monoecious plant, the low female-male flowers ratio and consequent low seed yield are the main bottlenecks for industrial-scale development of seed utilization. MiRNAs play crucial regulatory roles in flower development and sex differentiation; therefore, we evaluated the roles of miRNAs in the critical period of sex differentiation in X. sorbifolium. Materials and Methods: Four small RNA libraries for female and male flower buds of the critical period of sex differentiation were constructed from paraffin-embedded sections. The miRNAs were characterized by high-throughput sequencing, and differentially expressed miRNAs were validated by reverse transcription-quantitative polymerase chain reaction. Results: There were obvious differences in male and female pistil and stamen flower buds, with elongated inflorescence and clear separation of flower buds marking the critical period of sex differentiation. A total of 1619 conserved miRNAs (belonging to 34 families) and 219 novel miRNAs were identified. Among these, 162 conserved and 14 novel miRNAs exhibited significant differential expression in the four libraries, and 1677 putative target genes of 112 differentially expressed miRNAs were predicted. These target genes were involved in diverse developmental and metabolic processes, including 17 miRNAs directly associated with flower and gametophyte development, mainly associated with carbohydrate metabolism and glycan biosynthesis and metabolism pathways. Some miRNA functions were confirmed, and others were found to be complemented. Conclusions: Multiple miRNAs closely related to sex differentiation in X. sorbifolium were identified. The theoretical framework presented herein might guide sex ratio regulation to enhance seed yield.