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Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense ( AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined., Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (s RNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple ( Malus × domestica)., The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3′ UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) si RNAs, and that the s RNA coverage depth varies with the level of AS transcript expression., Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of s RNA biogenesis in plants. [ABSTRACT FROM AUTHOR]