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Background   Brassica rapa  includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and  cis -NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in  B. rapa  are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in  B. rapa . Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in  B. rapa .    Results  Analyses of four RNA sequencing datasets revealed 1031  cis -NATs  B. rapa  ssp.  chinensis  cv Wut and  B. rapa  ssp.  pekinensis  cv. Bre. Based on sequence homology between  Arabidopsis thaliana  and  B. rapa , 303 conserved  cis -NATs in  B. rapa  were found to correspond to 280 cis-NATs in  Arabidopsi s; the remaining 728 novel  cis -NATs were identified as  Brassica -specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150  cis -NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated.    Conclusions  Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in  B. rapa ; these sRNAs are potentially useful for the genetic improvement of heat tolerance in  B. rapa  and other crops.

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa