The aim of this study was to facilitate gene discovery for functional genome studies and to identify simple sequence repeat (SSR) markers for molecular-assisted selection in Phellinus linteus. The transcriptome of Phellinus linteus was sequenced using а high-throughput RNA sequencing system – the Illumina Hiseq 2000. A total of 16,383,818 clean sequencing reads, 35,532 contigs and 25,811 unigenes were postulated. Based on similarity searches with known proteins, 19,350 genes (74.97% of the unigenes) were annotated. In the present research, 19,266, 10,978 and 7831 unigenes were mapped in Nr, Swiss-Prot and clusters of orthologous groups (COG) classifications, respectively. Of all unigenes, 6845 were categorized into three functional groups, namely biological process, cellular components and molecular function and 11,088 were annotated to 108 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 1129 SSRs were identified in these unigenes. In addition, 23 candidate genes, potentially involved in sterol biosynthesis, were identified and were worthy of further investigation.

Summary Fruit shape is an important quality and yield trait in melon. Although some fruit shape-related QTLs have been reported in melon, the target genes and the underlying mechanism remain poorly understood. Here, we identified and characterized a gene controlling fruit shape from two melon inbred lines B8 and HP22. Genetic analysis suggests that the fruit shape was controlled by a single and incompletely dominant locus, designated CmFSI8/CmOFP13. The CmFSI8/CmOFP13 gene was finely mapped to a 53.7 kb interval on chromosome 8 based on BSA-seq and map-based cloning strategies. CmFSI8/CmOFP13 encodes an OVATE family protein (OFP) and is orthologous to AtOFP1 and SlOFP20. The transcription level of CmFSI8/CmOFP13 in the ovary of HP22 was significantly higher than that in B8. Sequence analysis showed that a 12.5 kb genomic variation with retrotransposon insertion identified in the promoter was responsible for elevating the expression of CmFSI8/CmOFP13, which ultimately caused the differences in fruit shape. Moreover, ectopic overexpression of CmFSI8/CmOFP13 in Arabidopsis led to multiple phenotypic changes, including kidney-shaped leaves and shortened siliques. Taken together, we have demonstrated the involvement of an OFP protein in regulating melon fruit shape, and understanding the molecular mechanism will enable us to better manipulate melon fruit shape in breeding.

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