Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum.
Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum.
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小麦中新型真菌响应性 lincRNA 的全基因组鉴定和功能预测
DOI：
10.1186/s12864-016-2570-0
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发表时间：
2016-03-15
期刊：
影响因子：
4.4
通讯作者：
Ji W
中科院分区：
文献类型：
--
作者：
Zhang H;Hu W;Hao J;Lv S;Wang C;Tong W;Wang Y;Wang Y;Liu X;Ji W
背景：条锈菌(Puccinia striiformis f.Tritici；Pst)和白粉病(Blumeria graminis f.sp.)小麦(Tritici；BGT)是小麦(Triticum Aestivum)的重要病害。越来越多的证据表明，长基因间的ncRNAs(LincRNAs)受发育调控，在植物的发育和逆境反应中发挥重要作用。结果：对六倍体小麦品系N9134在接种PST小种CyR31和BGT小种E09后1、2、3d的转录组进行重排，检测到lincRNAs。从58218个可能的lincRNA中鉴定出283个差异表达的lincRNA，占转录组的31.2%。其中有254个DE-lincRNAs对BGT胁迫有反应，52个在PST中有反应。其中，共检测到1328个SNRNP基序(sm位点)，分别含有RRU4-11RR sm位基序和RRU1-9VU1-7RR基序，其中尿苷总量大于3个但小于11个。此外，psRNatarget预测了101个DE-lincRNAs作为miRNA的靶标，而在TAPIR中发现了5个靶标模体。结论：综上所述，小麦lincRNA响应BGT和PST胁迫，在与miRNA的剪接和相互调控中发挥重要作用。小麦的sm位点比哺乳动物和模式植物的sm位点结构更复杂。本研究中产生的质量序列数据为未来小麦-真菌相互作用的功能和分子研究提供了线索。
Background: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.Results: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.Conclusions: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.