Identification of alternative splicing events by RNA sequencing in early growth XXXX fruits.

@entity4373 @entity523
BACKGROUND: @entity4373 ( @entity4373 ) regulates multiple biological processes including flowering, circadian and stress response in plant. Although accumulating evidences indicate that @entity4373 is developmentally regulated, how @entity4373 responds to developmental cues is not well understood. 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. High throughput RNA sequencing (RNA-seq) technology is advancing the genome-wide analysis of @entity4373 events in plant species, but the landscape of @entity4373 in early growth fruit is still not available for @entity523 ( @entity523 ), a model plant for fleshy fruit development study. RESULTS: Using RNA-seq, we surveyed the @entity4373 patterns in @entity523 seedlings, flowers and young developing fruits and found that 59.3  % of expressed multi-exon genes underwent @entity4373 in these tissues. The predominant type of @entity4373 events is intron retention, followed by alternative splice donor and acceptor, whereas exon skipping has the lowest frequency. Although the frequencies of @entity4373 events are similar among seedlings, flowers and early growth fruits, the fruits generated more splice variants per gene. Further comparison of gene expression in early growth fruits at 2, 5 and 10  days post anthesis revealed that 5206 multi-exon genes had at least one splice variants differentially expressed during early fruit development, whereas only 1059 out of them showed differential expression at gene level. We also identified 27 multi-exon genes showing differential splicing during early fruit growth. In addition, the study discovered 2507 new transcription regions (NTRs) unlinked to the annotated chromosomal regions, from where 956 putative protein coding transcripts and 1690 putative long non-coding RNAs were identified. CONCLUSIONS: Our genome-wide analysis of @entity4373 events reveals a distinctive @entity4373 pattern in early growth @entity523 fruits. The landscape of @entity4373 obtained in this study will facilitate future investigation on transcriptome complexity and @entity4373 regulation during early fruit growth in @entity523 . The newly found NTRs will also be useful for updating the @entity523 genome annotation.
