Long non-coding RNA(lncRNA)has been proved to be crucial in diverse biological processes of human beings.Though next generation sequencing(NGS)detects plenty of lncRNAs in plants,few cases was reported on their biological functions,including COOLAIR and COLDAIR controlling expression of FLC in Arabidopsis thaliana,AK111270 repressing LDMAR in rice(Oryza sativa).SUN,encoding a member of calmodulin binding protein family containing IQ domains,controls the elongated fruit shape of tomato(Solanum lycopersicum).The sun locus has been proposed to result from 24.7 kb duplication mediated by retrotransposon Rider,however,how the long transcript was formed remained unknown.To proclaim the mechanism,we introduced the sun locus into the wild species LA1589(Solanum pimpinellifolium)to obtain near isogenic lines(NILs)of sun.In this study,using the sun NILs we identified a lncRNA located on the intergenic region between sun and RecA by Northern blot and RT-PCR.Gene-specific RT-PCR suggested this lncRNA transcript derived from overlapped 3-ends of sun and RecA,however 3-RACE showed mature RNAs of these two genes were not overlapping.Moreover,RNA-seq data confirmed the existence of this lncRNA,and PCR-Southern blot indicated that part of it lacks ploy(A)tail.Furthermore,RNAi using sequences of this lncRNA caused significant changes in fruit shape through a mechanism remaining to be unraveled.Overall,our work may shed light on the formation of the sun locus in tomato and leads to better understanding of lncRNA.