Zhang Hong, Hu Weiguo, Hao Jilei, Lv Shikai, Wang Changyou, Tong Wei, Wang Yajuan, Wang Yanzhen, Liu Xinlun, Ji Wanquan
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
National Laboratory of Wheat Engineering, Institute of Wheat, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
BMC Genomics. 2016 Mar 15;17:238. doi: 10.1186/s12864-016-2570-0.
Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Increasingly evidences suggest that long intergenic ncRNAs (lincRNAs) are developmentally regulated and play important roles in development and stress responses of plants. However, identification of lincRNAs in wheat is still limited comparing with functional gene expression.
The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese Pst race CYR31 and Bgt race E09 at 1, 2, and 3 days post-inoculation was recapitulated to detect the lincRNAs. Here, 283 differential expressed lincRNAs were identified from 58218 putative lincRNAs, which account for 31.2% of transcriptome. Of which, 254 DE-LincRNAs responded to the Bgt stress, and 52 lincRNAs in Pst. Among them, 1328 SnRNP motifs (sm sites) were detected and showed RRU4-11RR sm site element and consensus RRU1-9VU1-7RR SnRNP motifs, where the total number of uridine was more than 3 but less than 11. Additionally, 101 DE-lincRNAs were predicted as targets of miRNA by psRNATarget, while 5 target mimics were identified using target mimicry search in TAPIR.
Taken together, our findings indicate that the lincRNA of wheat responded to Bgt and Pst stress and played important roles in splicesome and inter-regulating with miRNA. The sm site of wheat showed a more complex construction than that in mammal and model plant. The mass sequence data generated in this study provide a cue for future functional and molecular research on wheat-fungus interactions.
条锈病（条形柄锈菌小麦专化型；Pst）和白粉病（禾本科布氏白粉菌小麦专化型；Bgt）是全球小麦（普通小麦）的重要病害。越来越多的证据表明，长链基因间非编码RNA（lincRNAs）受到发育调控，并在植物发育和应激反应中发挥重要作用。然而，与功能基因表达相比，小麦中lincRNAs的鉴定仍然有限。
对六倍体小麦品系N9134在接种中国Pst小种CYR31和Bgt小种E09后1、2和3天的转录组进行概括分析以检测lincRNAs。在此，从58218个假定的lincRNAs中鉴定出283个差异表达的lincRNAs，占转录组的31.2%。其中，254个DE-LincRNAs对Bgt胁迫有响应，52个lincRNAs对Pst有响应。其中，检测到1328个SnRNP基序（sm位点），显示出RRU4-11RR sm位点元件和共有RRU1-9VU1-7RR SnRNP基序，其中尿苷总数超过3但少于11。此外，psRNATarget预测101个DE-lincRNAs为miRNA的靶标，而使用TAPIR中的靶标模拟搜索鉴定出5个靶标模拟物。
综上所述，我们的研究结果表明，小麦的lincRNA对Bgt和Pst胁迫有响应，并在剪接体以及与miRNA的相互调控中发挥重要作用。小麦的sm位点显示出比哺乳动物和模式植物中更复杂的结构。本研究产生的大量序列数据为未来小麦与真菌相互作用的功能和分子研究提供了线索。
