Krivmane Baiba, Ruņģis Dainis Edgars
Latvian State Forest Research Institute "Silava", 111 Rigas St., LV-2169 Salaspils, Latvia.
Genes (Basel). 2024 Dec 27;16(1):26. doi: 10.3390/genes16010026.
Methyl jasmonate is a plant signaling molecule involved in a wide range of functions, including stress responses. This study investigates the relative differential expression of microRNAs and their target genes in response to methyl jasmonate treatment of Scots pine needles. A combined strategy of high-throughput sequencing and in silico prediction of potential target genes was implemented. a total of 58 differentially expressed (DE) microRNAs (miRNAs) (43 up-regulated and 15 down-regulated), belonging to 29 miRNA families, were identified. The 41 DE miRNAs from 17 families were conifer-specific miRNA families-miR946, miR947, miR950, miR1312, miR1313, miR1314, miR3693, miR3107, miR11452, miR11466, miR11487, miR11490, miR11504, miR11511, miR11532, miR11544, and miR11551. The other DE miRNAs (miR159, miR164, miR169, miR396, miR397, miR398, miR408, miR535) were conserved miRNAs, which are also found in angiosperm species. Transcriptome analysis identified 389 gene transcripts with 562 miRNA-target sites targeted by 57 of the 58 DE miRNAs. Of these, 250 target genes with 138 different GO annotations were found for the 41 DE conifer-specific conserved miRNAs. The 26 DE miRNAs from 14 DE miRNA families, of which almost all (12 families, 24 miRNAs) are conifer specific, and were associated with 68 disease resistance and TMV resistance proteins, TIR-NBS-LRR, LRR receptor-like serine/threonine-protein kinase, putative CC-NBS-LRR protein, and putative NBS-LRR protein target transcripts with 29 target gene GO term descriptions. Some of the genes targeted by conifer-specific miRNAs have been previously reported to be targeted by other miRNAs in angiosperms, indicating that the miRNA-target gene regulation system can vary between species.
茉莉酸甲酯是一种植物信号分子，参与包括应激反应在内的多种功能。本研究调查了在茉莉酸甲酯处理欧洲赤松针叶后，微小RNA（miRNA）及其靶基因的相对差异表达。实施了高通量测序和潜在靶基因的电子预测相结合的策略。共鉴定出58个差异表达（DE）的miRNA，属于29个miRNA家族（43个上调和15个下调）。来自17个家族的41个DE miRNA是针叶树特异性miRNA家族——miR946、miR947、miR950、miR1312、miR1313、miR1314、miR3693、miR3107、miR11452、miR11466、miR11487、miR11490、miR11504、miR11511、miR11532、miR11544和miR11551。其他DE miRNA（miR159、miR164、miR169、miR396、miR397、miR398、miR408、miR535）是保守的miRNA，在被子植物物种中也有发现。转录组分析鉴定出389个基因转录本，具有562个miRNA靶位点，被58个DE miRNA中的57个靶向。其中，针对41个DE针叶树特异性保守miRNA发现了250个具有138种不同基因本体论（GO）注释的靶基因。来自14个DE miRNA家族的26个DE miRNA，其中几乎所有（12个家族，24个miRNA）都是针叶树特异性的，并且与68种抗病和烟草花叶病毒（TMV）抗性蛋白、TIR-NBS-LRR、LRR受体样丝氨酸/苏氨酸蛋白激酶、假定的CC-NBS-LRR蛋白和假定的NBS-LRR蛋白靶转录本相关，具有29个靶基因GO术语描述。针叶树特异性miRNA靶向的一些基因先前已报道在被子植物中被其他miRNA靶向，这表明miRNA-靶基因调控系统在不同物种之间可能有所不同。
