Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741
Abstract
:1. Introduction
2. Results
2.1. Analysis of mRNA and lncRNA Expression under Different Light Types
2.2. Identification and Analysis of Differentially Expressed lncRNAs
2.3. GO and KEGG Analyses of the Differentially Expressed lncRNAs Target Genes
2.4. Target Gene Prediction Based on Differentially Expressed lncRNAs
2.5. Verification of Differentially Expressed lncRNAs
2.6. Verification of Differentially Expressed lncRNAs and Target Gene Expression
2.7. lncRNA-miRNA-mRNA Expression Pattern Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. cDNA Library Construction, Sequencing, and Transcript Assembly
4.3. Identification of lncRNAs
4.4. Differential lncRNA Expression Analysis
4.5. Differentially Expressed lncRNAs as miRNA Targets: Prediction of Their Target Genes
4.6. qRT-PCR Validation of Differentially Expressed lncRNAs and Target Genes
4.7. LncRNA-miRNA-mRNA Expression Pattern Validation
4.8. Analysis of Protein Expression in Poplar Leaves Using Western Blotting
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Read | Base | Q 20% | Q 30% | GC Content% | |
---|---|---|---|---|---|
WHT-1 | 46155433 | 6.9G | 98.57% | 95.68% | 53% |
WHT-2 | 37327425 | 5.6G | 98.61% | 95.74% | 53% |
WHT-3 | 42099884 | 6.3G | 98.55% | 95.62% | 53% |
LBL-1 | 34499736 | 5.2G | 98.58% | 95.65% | 52% |
LBL-2 | 51038681 | 7.6G | 98.57% | 95.67% | 53% |
LBL-3 | 40665290 | 6.1G | 98.56% | 95.68% | 52% |
No. | lnc Gene | mRNA_GeneName | mRNA_Region | Strand_Status | Up or Down |
---|---|---|---|---|---|
1 | MSTRG.23213.1 | POPTRDRAFT_0006s24570 | cds | antisense | up |
2 | MSTRG.20734.2 | POPTRDRAFT_580797 | cds | antisense | |
MSTRG.20734.2 | POPTRDRAFT_580797 | cds | antisense | up | |
MSTRG.20734.2 | POPTRDRAFT_580797 | utr5 | antisense | ||
3 | MSTRG.24413.1 | POPTRDRAFT_1083565 | downstream2K | sense | |
MSTRG.24413.1 | POPTRDRAFT_1083561 | upstream2K | sense | up | |
MSTRG.24413.1 | POPTRDRAFT_1083565 | utr3 | sense | ||
MSTRG.24413.1 | POPTRDRAFT_1083565 | cds | sense | ||
MSTRG.24413.1 | POPTRDRAFT_1083565 | utr5 | sense | ||
4 | MSTRG.7072.1 | MSTRG.7071 | exonic | antisense | down |
MSTRG.7072.1 | MSTRG.7071 | intronic | antisense | ||
5 | MSTRG.14802.1 | POPTRDRAFT_550790 | cds | antisense | |
MSTRG.14802.1 | MSTRG.14809 | intronic | antisense | up | |
MSTRG.14802.1 | POPTRDRAFT_753933 | intronic | antisense | ||
6 | MSTRG.14565.3 | POPTRDRAFT_580392 | exonic | sense | |
MSTRG.14565.3 | POPTRDRAFT_580392 | intronic | sense | up | |
MSTRG.14565.3 | POPTRDRAFT_580392 | downstream2K | sense | ||
7 | MSTRG.9936.2 | MSTRG.9934 | downstream2K | sense | up |
MSTRG.9936.2 | POPTRDRAFT_580622 | cds | antisense | ||
MSTRG.9936.2 | MSTRG.9934 | downstream2K | sense | ||
MSTRG.9936.2 | POPTRDRAFT_580622 | intronic | antisense | ||
8 | MSTRG.25033.1 | down | |||
9 | MSTRG.20413.1 | up |
lnc RNA | Target Gene | Function Notes |
---|---|---|
MSTRG.20734.2 | POPTR_0005s15660.1 | Predictive protein |
MSTRG.7072.1 | MSTRG.7071.1 | Calmodulin binding protein |
MSTRG.9936.2 | POPTR_0015s05360.3 | Interaction protein: chlorophyll A-B binding protein (Lhca3) Interaction protein: chlorophyll A-B binding protein (Lhca6) |
POPTR_0015s05360.4 |
miRNA Acc. | Target Acc. LncRNA | Alignment | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ptc-miR156h | LOC7487123 | miRNA | 21 | C A | C G | A G | A G | A U | A G | A A | G A | C A | G U | U | 1 |
: : | : | : | : : | : : | : : | : : | . : | : : | : : | ||||||
Target | 762 | G U | C C | U G | U C | U A | U C | U U | U U | G U | C A | U | 782 | ||
ptc-miR166c | LOC112328927 | miRNA | 21 | C C | C C | U U | A C | U U | C G | G A | C C | A G | G C | U | 1 |
: : | : : | : : | : : | : : | : : | : : | : : | : : | : : | : | |||||
Target | 301 | G G | G G | A A | U G | A A | G C | C U | G G | U C | C G | A | 321 | ||
ptc-miR166e | miRNA | 21 | C C | C C | U U | A C | U U | C G | G A | C C | A G | G C | U | 1 | |
: : | : : | : : | : : | : : | : : | : : | : : | : : | : : | : | |||||
Target | 301 | G G | G G | A A | U G | A A | G C | C U | G G | U C | C G | A | 321 | ||
ptc-miR166i | miRNA | 21 | C C | C C | U U | A C | U U | C G | G A | C C | A G | G C | U | 1 | |
: : | : : | : : | : : | : : | : : | : : | : : | : : | : : | : | |||||
Target | 301 | G G | G G | A A | U G | A A | G C | C U | G G | U C | C G | A | 321 | ||
ptc-miR167b | MSTRG.25033.1 | miRNA | 21 | A U | C U | A G | U A | C G | A C | C G | U C | G A | A G | U | 1 |
: : | : : | : | : : | : : | : | : : | : : | : | : : | : | |||||
Target | 1654 | U A | G A | U -- | A U | G C | U U | G C | A G | C G | U C | A | 1673 | ||
ptc-miR167f-5p | miRNA | 21 | U U | C U | A G | U A | C G | A C | C G | U C | G A | A G | U | 1 | |
: | : : | : | : : | : : | : | : : | : : | : | : : | : | |||||
Target | 1654 | U A | G A | U -- | A U | G C | U U | G C | A G | C G | U C | A | 1673 | ||
ptc-miR319a | LOC112325201 | miRNA | 20 | U U | C U | C G | A G | G G | A A | G U | A G | G U | U U | 1 | |
: : | : : | : | . | : . | : : | : : | : : | : | : . | ||||||
Target | 521 | G G | G A | U C | A U | C U | U U | C A | G U | C A | A G | 540 | |||
ptc-miR319d | miRNA | 20 | U U | C U | C G | A G | G G | A A | G U | A G | G U | U U | 1 | ||
: : | : : | : | . | : . | : : | : : | : : | : | : . | ||||||
Target | 521 | G G | G A | U C | A U | C U | U U | C A | G U | C A | A G | 540 | |||
ptc-miR396c | MSTRG.20413.1 | miRNA | 21 | U U | C A | A G | U U | C U | U U | C G | A C | A C | C U | U | 1 |
: : | : : | : : | . . | : | : : | : : | : : | . | |||||||
Target | 1159 | G A | A A | U C | A A | G A | G G | G A | U G | U G | G A | G | 1179 | ||
ptc-miR396e-5p | miRNA | 21 | U U | C A | A G | U U | C U | U U | C G | A C | A C | C U | U | 1 | |
: : | : : | : : | . . | : | : : | : : | : : | . | |||||||
Target | 1159 | G A | A A | U C | A A | G A | G G | G A | U G | U G | G A | G | 1179 | ||
ptc-miR403b | LOC7481412 | miRNA | 21 | G C | U C | A A | A C | A C | G C | A C | U U | A G | A U | U | 1 |
: | . : | : : | : : | : : | : | : : | : : | : : | : : | : | |||||
Target | 278 | C A | G G | U U | U G | U G | C A | U G | A A | U C | U A | A | 298 | ||
ptc-miR403c-3p | miRNA | 21 | G C | U C | A A | A C | A C | G C | A C | U U | A G | A U | U | 1 | |
: | . : | : : | : : | : : | : | : : | : : | : : | : : | : | |||||
Target | 278 | C A | G G | U U | U G | U G | C A | U G | A A | U C | U A | A | 298 |
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Li, H.; Zhang, Y.; Lan, J.; Wang, S.; Cai, H.; Meng, X.; Ren, Y.; Yang, M. Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741. Plants 2023, 12, 3157. https://doi.org/10.3390/plants12173157
Li H, Zhang Y, Lan J, Wang S, Cai H, Meng X, Ren Y, Yang M. Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741. Plants. 2023; 12(17):3157. https://doi.org/10.3390/plants12173157
Chicago/Turabian StyleLi, Hongyan, Yiwen Zhang, Jinping Lan, Shijie Wang, Hongyu Cai, Xin Meng, Yachao Ren, and Minsheng Yang. 2023. "Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis of Populus tomentosa Hybrid Poplar 741" Plants 12, no. 17: 3157. https://doi.org/10.3390/plants12173157