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Early fruit growth mainly characterized by active cell division and cell expansion contributes to the formation of fruit morphology and quality traits.Transcriptome profiling has revealed the coordinated complex regulation of gene expression in the process.Alternative splicing(AS)regulates multiple biological processes including flowering,circadian and stress response in plant.Although accumulating evidences indicate that AS is developmentally regulated,how AS responds to developmental cues is not well understood.High throughput RNA sequencing(RNA-seq)technology is advancing the genome-wide analysis of AS events in plant species,but the landscape of alternative splicing in early growth fruit is still not available for tomato(Solanum lycopersicum),a model plant for fleshy fruit development study.Using RNA-seq,we surveyed the AS patterns in tomato seedlings,flowers and young developing fruits and found that 59.3%of expressed multi-exon genes underwent AS in these tissues.Comparison of gene expression in early growth fruits at 2,5 and 10 days post anthesis(dpa)revealed that 5,206multi-exon genes had at least one splice variants differentially expressed during early fruit development,whereas only 1,059 out of them showed differential expression at gene level.We also identified 27 multiexon genes showing differential splicing during early fruit growth.In addition,the study discovered 2,507 new transcription regions(NTRs)unlinked to the annotated chromosomal regions,producing 956 putative protein coding transcripts and 1,690 putative long non-coding RNA(lncRNAs).Our genome-wide analysis of alternative splicing reveals a distinctive AS pattern in early growth tomato fruits.The landscape of AS obtained in this study will facilitate future investigation on transcriptome complexity and AS regulation during early fruit growth in tomato.The newly found NTRs will also be useful for updating the tomato genome annotation.