MicroRNAs as regulators of gene expression have been known for over a decade and have been correlated with various types of abiotic and biotic stresses. IsomiRs are modified forms of typical miRNAs altered by one or few nucleotides as a result of post transcriptional modifications of miRNAs at terminals or SNPs containing miRNA sequences producing 5′/3′ isomiRs or SNP_isomiRs. These isoforms function exactly like miRNAs, but sometimes alter the target gene preference particularly when they differ in sequences within seed region. Existence of isomiRs was considered earlier as errors in sequencing techniques due to unavailability of proper detection tools. Bread wheat is the most cultivated cereal crop globally with a strong hold on world’s economy. Wheat production is frequently affected by rust diseases. Leaf rust, caused by Puccinia triticina, severely affects grain filling. Four small RNA libraries were prepared from leaves of two wheat Near Isogenic Lines, HD2329 (susceptible) and HD2329 + Lr24 (resistant) both under mock- and pathogen-inoculated conditions and sequenced using Illumina NGS. Several novel miRNAs were detected from these sequences. The present study focuses on identification of isomiRs derived from these miRNAs and their target genes. In total, 66 and 38 unique 5′ and 3′ isomiRs respectively were identified from 37 miRNAs. IsomiRs targeted genes with functions like amino acid metabolism, replication, transport, chelation of reactive oxygen species in wheat while genes with SunT and Structural Maintenance of Chromosome domain of Puccinia. This study will provide a basis for exploitation of isomiRs for genetic improvements in wheat.

中文翻译：

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小麦和小麦锈病中叶锈反应小麦IsomiRs及其靶基因的鉴定与验证

微小RNA作为基因表达的调节剂已经有十多年的历史了，并且与各种非生物和生物胁迫相关。IsomiRs是典型miRNA的修饰形式，是由于miRNA在含有产生5'/ 3'isomiRs或SNP_isomiRs的miRNA序列的末端或SNP处的转录后修饰而改变的一个或几个核苷酸。这些亚型的功能与miRNA完全相同，但有时会改变靶基因的偏好，尤其是当它们在种子区域内的序列不同时。由于无法使用适当的检测工具，早期将isomiRs的存在视为测序技术中的错误。面包小麦是全球种植最多的谷物作物，在世界经济中占有重要地位。小麦产量经常受到锈病的影响。叶锈病，引起小麦锈菌，严重影响谷物的充实。在模拟和病原体接种条件下，从两个小麦近等基因系HD2329（易感）和HD2329 + Lr24（抗性）的小麦叶片中制备了四个小RNA文库， 并使用Illumina NGS进行了测序。从这些序列中检测到几种新颖的miRNA。本研究的重点是鉴定源自这些miRNA及其靶基因的isoomiR。总共从37个miRNA中分别鉴定出66个和38个独特的5'和3'isomiR。IsomiRs靶基因中包含氨基酸代谢，复制，传输，在小麦的活性氧物种的螯合功能，同时基因的染色体结构域的SUNT与结构维护柄锈菌。这项研究将为利用isoomiRs进行小麦遗传改良提供基础。