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In angiosperm plants, successful sexual reproduction requires recognition and communications between male and female gametophytes.We adopted high-throughput RNA sequencing to analyze the transcriptome profiles of both male and female gametophytes at different developmental stages in Arabidopsis.We were interested in signaling components involved in male-female interaction and identified 85 receptor-like kinase genes that are enriched in pollen tubes and 221 small peptide-encoding genes that were preferentially expressed in mature ovules.The role of the small peptide-encoding genes was demonstrated by two examples, EN 14 and EN 15,which were demonstrated to be female-secreted cues to affect interaction between pollen tube and ovule by genetic and biochemical approaches.The identification of the receptor-like kinases perceiving the EN signals would also be discussed.