Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and Extraction of RNA
2.2. Small RNA Enrichment, Library Preparation and Sequencing Analysis
2.3. Transcriptome Library Preparation and Sequencing Analysis
2.4. Data Analysis
2.5. Statistical Analysis
3. Results
3.1. Sequencing of Small RNA Libraries
3.2. Differentially Expressed microRNAs
3.3. Gene Ontology Annotation of Target Genes of Differentially Expressed microRNAs
3.4. Target Genes of Differentially Expressed Conifer-Specific microRNAs
3.5. Identification and Expression Analysis of Target Genes of Differentially Expressed microRNAs from Transcriptome Data
3.6. Resistance-Related Target Genes of Differentially Expressed microRNAs from Transcriptome Data
3.7. Analysis of Differentially Expressed microRNAs Targeting Differentially Expressed Gene Transcripts
4. Discussion
4.1. Differentially Expressed microRNAs in Conifers After Methyl Jasmonate Treatment
4.2. Predicted Target Genes for Differentially Expressed Down-Regulated microRNAs
4.3. Predicted Target Genes for Differentially Expressed Up-Regulated microRNAs
4.4. Differentially Expressed Pinus sylvestris Genes Targeted by Differentially Expressed microRNAs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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microRNA Family | microRNA Sequence | Mature microRNA Length (in Nucleotides) | Count of Precursor-microRNAs | Precursor-microRNA Accession Number |
---|---|---|---|---|
Up-regulated | ||||
miR00002 | GTTCGGAGAAATGCGTGCTCG | 21 | 1 | TC188772 |
miR00024 | CGTGTTCCCAGGTCGCCCGG | 20 | 1 | TC188772 |
miR00024 | CGTGTTCCCAGGTCACCCAG | 20 | 1 | TC188772 |
miR00024 | CGTGTTCCCAGGTCGCCCCGG | 21 | 1 | TC188772 |
miR00028 | ATGTGAGAAAAGGGTTTGTGG | 21 | 1 | AW010185 |
miR11452 * | TGGGAGCGATCGATGAGGTGTT | 22 | - | - |
miR11466 * | CGATCTCCAGAAGACACTTGT | 21 | - | - |
miR11487 * | CATATTGATCGCCTTCTCAGT | 21 | - | - |
miR11487 * | TCATATTGATCGCCTTCTCAG | 21 | - | - |
miR11487 * | TGAGAAAGCGATCAACATGAC | 21 | - | - |
miR11487 * | TGAGAAGGCGATCAACATGAC | 21 | - | - |
miR11487 * | TGAGAAGGCGATCAACATGAT | 21 | - | - |
miR11487 * | TGAGAAGGCGATCAACATGC | 20 | - | - |
miR11504 * | AATGAGCTCCTCCTCATGTCC | 21 | - | - |
miR11504 * | AATGAGCTCCTCCTCATGTCT | 21 | - | - |
miR11511 * | TCCAACGAAGATCAGAAAGG | 21 | - | - |
miR11511 * | TCCAACGAAGATCAGAAGGC | 20 | - | - |
miR11511 * | TCCAACGAAGATCAGAAGGCGT | 22 | - | - |
miR11511 * | TCCAACGAAGATCAGAAGGCTC | 22 | - | - |
miR11511 * | TCCACCGAAGATCAGAAGGTTC | 22 | - | - |
miR11511 * | TCCACCGAAGATCAGAAGGTTTT | 23 | - | - |
miR11544 * | TGGAGCTGTTGTCACTCCACT | 21 | - | - |
miR11551 * | TGTTTTGCTTTCCCTCCGCAAT | 22 | - | - |
miR1312 * | TCGGAGAGAATATGGCGAGAT | 21 | - | - |
miR1313 * | AACAATAATTTCAGTGGAAGA | 21 | 2 | CO167297, DR013032 |
miR1314 * | TCGGCCTCGAAATGTTAGGAGAA | 23 | - | - |
miR159 | TTTGGTTTGAAGGGAGCTCCA | 21 | - | - |
miR159 | CTTGGATTGAAGGGAGCTCC | 20 | 1 | DR078315 |
miR159 | TTTGGTTTGAAGGGAGCTCT | 20 | - | - |
miR164 | TGGAGAAGCAGGGCACGTGCG | 21 | - | - |
miR169 | GGCAAGTTGTTCTTGGCAAAG | 21 | - | - |
miR3693 * | CTGAACTGCTTATAGATGGGA | 21 | - | - |
miR3693 * | TGAACTGCTTATAGATGGGAG | 21 | - | - |
miR396 | CTCAAAGAAAGCTGTGGGAAA | 21 | - | - |
miR398 | ACGTGTTCCCAGGTCACCCCA | 21 | 2 | TC184482, TC188772 |
miR398 | CGTGTTCCCAGGTCACCCCAG | 21 | 2 | TC184482, TC188772 |
miR408 | TGCACTGCCTCTTCCCTGGCT | 21 | 2 | TC159922, TC180357 |
miR6171 | TGTGGATTGCTGAAGGATTTA | 21 | - | - |
miR946 * | TGTGGATAGAGAAGGGTTAGT | 21 | - | - |
miR947 * | CATCGGAATCTGTTACTGTTTT | 22 | - | - |
miR947 * | CATCGGAATCTGTTACTGTTTC | 22 | - | - |
miR947 * | CATCGGAATCTGTTACTGTTT | 21 | - | - |
miR950 * | TCTGGTCCTCGGTGGTTTATGAAT | 24 | - | - |
Down-regulated | ||||
miR11466 * | CACTTCCAATAGACACTTGTT | 21 | - | - |
miR11466 * | TCTACTTCCACAAGACACTTGCC | 23 | - | - |
miR11490 * | TAGCCCGAACGCACAATTGGA | 21 | - | - |
miR11532 * | TGACATTGTAAAGTACGGGAAT | 22 | - | - |
miR3701 * | TAAACAATGTCCACCCTTCATT | 22 | - | - |
miR397 | TCATCATTGAGTGCAGCATTG | 21 | - | - |
miR535 | TCGACAACGAGAGAGAGCACGC | 22 | - | - |
miR946 * | TCAGACCTTCTCCTATCCACAAT | 23 | - | - |
miR946 * | CAGCCCTTCTCCTATCCACCAAC | 23 | - | - |
miR946 * | TAGACCTTCTCCTATCCACCAAT | 23 | - | - |
miR950 * | TCACATCTAGGCCACGATGGTT | 22 | - | - |
miR950 * | TCACGTCTGGGCCTCTATGGTT | 22 | - | - |
miR950 * | TCGTGTCCTCGGTGGTTTATGA | 22 | - | - |
miR950 * | TTTACGTCTGGTCCTCGATGGTT | 23 | - | - |
miR950 * | TTACATCTGGGCCACGGTGGTT | 22 | 1 | TC178188 |
microRNA Family | Pinus sylvestris | Taxus chinensis | Taxus × Media | Picea abies |
---|---|---|---|---|
miR156 | - | down | down | - |
miR159 | up | - | - | - |
miR162 | - | - | - | down |
miR164 | up | up | up | - |
miR167 | - | - | - | down |
miR168 | - | down | down | - |
miR169 | up | down | down | up |
miR172 | - | down | down | up |
miR319 | - | - | - | down |
miR390 | - | up | up | up |
miR396 | up | down | down | down |
miR397 | down | - | - | up |
miR398 | up | - | - | up |
miR398 | - | - | - | up |
miR399 | - | - | - | - |
miR408 | up | - | down | - |
miR437 | - | - | - | up |
miR480 | - | down | - | - |
miR482 | - | - | - | up |
miR529 | - | - | - | down |
miR535 | down | - | - | - |
miR858 | - | - | - | up |
miR946 | down/up | - | - | - |
miR947 | up | - | - | - |
miR950 | down/up | - | - | up |
miR1310 | - | down | - | - |
miR1311 | - | - | - | up |
miR1312 | up | - | - | - |
miR1313 | up | - | - | down |
miR1314 | up | - | - | - |
miR3693 | up | - | - | up |
miR3701 | down | - | - | up |
miR4376 | - | - | - | up |
miR6171 | up | - | - | - |
miR00002 | up | - | - | - |
miR00024 | up | - | - | - |
miR00028 | up | - | - | - |
miR11452 | up | - | - | - |
miR11466 | down/up | - | - | - |
miR11467 | - | - | - | down |
miR11487 | up | - | - | up |
miR11490 | down | - | - | - |
miR11498 | - | - | - | down |
miR11504 | up | - | - | - |
miR11511 | up | - | - | - |
miR11524 | - | - | - | up |
miR11532 | down | - | - | - |
miR11539 | - | - | - | up |
miR11544 | up | - | - | - |
miR11551 | up | - | - | up |
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Share and Cite
Krivmane, B.; Ruņģis, D.E. Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment. Genes 2025, 16, 26. https://doi.org/10.3390/genes16010026
Krivmane B, Ruņģis DE. Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment. Genes. 2025; 16(1):26. https://doi.org/10.3390/genes16010026
Chicago/Turabian StyleKrivmane, Baiba, and Dainis Edgars Ruņģis. 2025. "Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment" Genes 16, no. 1: 26. https://doi.org/10.3390/genes16010026
APA StyleKrivmane, B., & Ruņģis, D. E. (2025). Differential microRNA and Target Gene Expression in Scots Pine (Pinus sylvestris L.) Needles in Response to Methyl Jasmonate Treatment. Genes, 16(1), 26. https://doi.org/10.3390/genes16010026