title: Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa.
abstract: 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 Arabidopsis; 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.
authors: Xiang
authors: X
authors: Yu
authors: Jun
authors: J
authors: Yang
authors: Xiaorong
authors: X
authors: Li
authors: Xuxin
authors: X
authors: Liu
authors: Chuanbao
authors: C
authors: Sun
authors: Feijie
authors: F
authors: Wu
authors: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. ykhe@sibs.ac.cn.
authors: Yuke
authors: Y
authors: He
mesh_terms: D001937:Brassica / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D006358:Hot Temperature; D016372:RNA, Antisense / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D016372:RNA, Antisense; D034741:RNA, Small Interfering