Abstract
Seedlessness is a desirable character in lemons and other citrus species. Seedless fruit can be induced in many ways, including through self-incompatibility (SI). SI is widely used as an intraspecific reproductive barrier that prevents self-fertilization in flowering plants. Although there have been many studies on SI, its mechanism remains unclear. The ‘Xiangshui’ lemon is an important seedless cultivar whose seedlessness has been caused by SI. It is essential to identify genes involved in SI in ‘Xiangshui’ lemon to clarify its molecular mechanism. In this study, candidate genes associated with SI were identified using high-throughput Illumina RNA sequencing (RNA-seq). A total of 61,224 unigenes were obtained (average, 948 bp; N50 of 1,457 bp), among which 47,260 unigenes were annotated by comparison to six public databases (Nr, Nt, Swiss-Prot, KEGG, COG, and GO). Differentially expressed genes were identified by comparing the transcriptomes of no-, self-, and cross-pollinated stigmas with styles of the ‘Xiangshui’ lemon. Several differentially expressed genes that might be associated with SI were identified, such as those involved in pollen tube growth, programmed cell death, signal transduction, and transcription. NADPH oxidase genes associated with apoptosis were highly upregulated in the self-pollinated transcriptome. The expression pattern of 12 genes was analyzed by quantitative real-time polymerase chain reaction. A putative S-RNase gene was identified that had not been previously associated with self-pollen rejection in lemon or citrus. This study provided a transcriptome dataset for further studies of SI and seedless lemon breeding.
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Acknowledgments
We are grateful for the technical support for Illumina sequencing and the initial data analysis we received from the Beijing Genome Institute at Shenzhen, China. This research was supported by Guangxi Science Research and Technology Development Project (1123003-3C), the National Natural Science Foundation of China (31460508), and the Innovation Team of Guangxi Citrus Industry Project.
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All authors have read and approved the manuscript. It is not being submitted to any other journal. The authors have declared that no competing interests exist.
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Communicated by S. Hohmann.
Shuwei Zhang and Feng Ding contributed equally to this paper.
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438_2014_920_MOESM2_ESM.tif
Supplementary material 2 (TIFF 1,167 kb) Figure S2 Characteristics of the homology search of assembled unigenes against the NR databases. E-value distribution of the top BLAST hits for each unigene with a cut-off E-value of 1.0E−5 (A). Similarity distribution of BLAST hits for each unigene in the NR database (B)
438_2014_920_MOESM4_ESM.xls
Supplementary material 4 (XLS 22 kb) Table S2 List of important differential genes likely related to the self-incompatible process
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Zhang, S., Ding, F., He, X. et al. Characterization of the ‘Xiangshui’ lemon transcriptome by de novo assembly to discover genes associated with self-incompatibility. Mol Genet Genomics 290, 365–375 (2015). https://doi.org/10.1007/s00438-014-0920-7
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DOI: https://doi.org/10.1007/s00438-014-0920-7