RNA-seq detects 319 novel transcripts. (A) Novel transcripts detected by RNA-seq are identified on all chromosomes distributed as expected by chromosome size. (B) Novel transcripts (median size 315 bp) are much smaller than annotated FlyBase transcripts (median size 1560 bp). (C) The majority of novel transcripts identified in this study have two exons. (D) Clustering identifies many novel transcripts expressed at specific time points or in sex-specific patterns. For example, many novel transcripts are expressed in male but not female adults, although they are observed in mixed larva and pupa samples (Male). Other clusters express most abundantly in a specific stage (Larva). (E) A novel transcript is depicted, and the associated junction is supported by 50 sequenced reads. Experimental validation by RT-PCR was obtained in pupae cDNA (see Supplemental Fig. 2).
