Integrated SRNA-Seq and RNA-Seq Analysis Reveals the Regulatory Roles of miRNAs in the Low-Temperature Responses of Canarium album
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Methods
2.2.1. RNA Extraction and Quality Determination
2.2.2. Library Construction and Sequencing
2.2.3. Small RNA Data Analysis
2.2.4. Transcriptome Data Analysis
2.2.5. qRT-PCR Verification of DEMs and DEGs
3. Results
3.1. Phenotypic Changes of Cold-Tolerant and Susceptible C. album cultivars under LTS
3.2. Small RNA Sequencing Analysis
3.2.1. Overview of SRNA-Seq Data and Identification of Conserved miRNAs in C. album
3.2.2. Differential Expression Analysis of miRNAs
3.3. Comparative Transcriptome Analysis Results
3.3.1. RNA-Seq and De Novo Assembly of Transcriptome
3.3.2. DEGs Identification and Enrichment Analysis Results
3.4. Integrated Analysis of Differnetially Expresssed MiRNAs and MRNAs
3.4.1. KEGG Enrichment Analysis of DEM Target Genes
3.4.2. Expression Analysis of DEMs and Their Corresponding Target Genes
4. Discussion
4.1. Some miRNAs Contribute to the Cold-Tolerance of C. album
4.2. The Low Temperature Responses of C. ablum Involved Multiple Metabolic Pathways
4.3. The Interactions of Some MiRNAs and Their Target mRNAs Might Contributed Greatly to the Cold Resistance Response of C. album
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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ID | Primer Sequence (5′-3′) | Description | |
---|---|---|---|
Forward | Reverse | ||
TRINITY_DN10933_c0_g1 | TCTTTCTGGATTTGGGACC | TTCTTCACGCCCTTCAGTC | Scarecrow-like protein 6 |
TRINITY_DN1114_c0_g1 | TGTTTGGGTTCTATCGGAG | AGAGAGGGTTGGTGGTATTG | Heavy metal-associated isoprenylated plant protein 7 |
TRINITY_DN18405_c0_g1 | CTACACACCATTGCGGACT | GAAGAAACAGGACCATCGG | U-box domain-containing protein |
TRINITY_DN2165_c0_g2 | TTGCCGCCAGAGACATTAG | TACCAGAAGAAGTCCGAGCC | Scarecrow-like protein 6 |
TRINITY_DN24638_c0_g1 | CAAGCACCCATCTAACCTCT | ACTGGCTAAACTGCGAAACT | Laccase-17 |
TRINITY_DN4966_c0_g1 | GCCACGAATCCTCTATCTCC | TAGTGCCTTGTAACGCCTG | Laccase-4 |
TRINITY_DN4966_c0_g2 | TGGTCAGGGTTTCGGTAA | CAATCCAAGCCATCCTCA | Laccase-2 |
TRINITY_DN5262_c0_g1 | ATGGAATGACAGAGGCAGG | CAGAGAGGCACCAGTTTCA | 4-coumarate--CoA ligase 1 |
TRINITY_DN6730_c0_g1 | GGCTCACAACCGCTACTTT | CACATTCCGTCTCCGTTAC | E3 ubiquitin-protein ligase |
TRINITY_DN23504_c1_g1 | CAACAAGGGATAGATGCGT | ATTCCAAAGACAGACCTGCT | Suppressor of npr1-1, constitutive1 |
TRINITY_DN76209_c0_g1 | TGCCTTCAAACCACAACC | TGGAACATAAACAAGCGGAC | Auxin response factor 2A |
miRNA Name | Forward Primer Sequence (5′-3′) | miRNA Name | Forward Primer Sequence (5′-3′) |
---|---|---|---|
cal-miR171_2-1 | TTGAGCCGTGCCAATATC | cal-miR1446-1 | TTCTGAACTCTCTCCCTCAAC |
cal-miR397-3 | TGAGTGCAGCGTTGATGT | cal-miR171_2-6 | AGATATTGGTGCGGTTCAA |
cal-miR159-39 | TCTTGTAGTGAAGGGAGCTCT | cal-miR482-22 | TTTCCGACACCTCCCATT |
cal-miR394-1 | GGCATTCTGTCCACCTCC | cal-undef-8 | CGAAACCTGGCTCTGATACC |
cal-miR397-3 | TGAGTGCAGCGTTGATGTT | cal-undef-161 | TTCCCCAGTGGAGTCGC |
Pathway ID | Pathway | Up_Number | Down_Number | DEG_Number | Total_Number | p |
---|---|---|---|---|---|---|
ko00940 | Phenylpropanoid biosynthesis | 52 | 22 | 74 | 242 | 1.188 × 10−11 |
ko00906 | Carotenoid biosynthesis | 26 | 4 | 30 | 78 | 5.732 × 10−8 |
ko04075 | Plant hormone signal transduction | 53 | 51 | 104 | 455 | 1.035 × 10−7 |
ko00500 | Starch and sucrose metabolism | 59 | 17 | 76 | 333 | 5.521 × 10−6 |
ko00909 | Sesquiterpenoid and triterpenoid biosynthesis | 18 | 2 | 20 | 51 | 6.452 × 10−6 |
ko04626 | Plant-pathogen interaction | 38 | 76 | 114 | 571 | 2.705 × 10−5 |
ko04712 | Circadian rhythm-plant | 33 | 2 | 35 | 126 | 3.005 × 10−5 |
ko04016 | MAPK signaling pathway-plant | 17 | 38 | 55 | 242 | 1.157 × 10−4 |
ko00073 | Cutin, suberine and wax biosynthesis | 13 | 1 | 14 | 38 | 3.378 × 10−4 |
ko00780 | Biotin metabolism | 8 | 5 | 13 | 38 | 1.226 × 10−3 |
ko00630 | Glyoxylate and dicarboxylate metabolism | 37 | 10 | 47 | 228 | 3.039 × 10−3 |
ko00942 | Anthocyanin biosynthesis | 3 | 1 | 4 | 6 | 4.357 × 10−3 |
ko00260 | Glycine, serine and threonine metabolism | 31 | 8 | 39 | 185 | 4.393 × 10−3 |
ko00941 | Flavonoid biosynthesis | 17 | 0 | 17 | 66 | 7.264 × 10−3 |
ko00943 | Isoflavonoid biosynthesis | 0 | 3 | 3 | 4 | 9.510 × 10−3 |
ko00052 | Galactose metabolism | 18 | 11 | 29 | 138 | 0.013 |
ko00480 | Glutathione metabolism | 15 | 27 | 42 | 217 | 0.015 |
ko00520 | Amino sugar and nucleotide sugar metabolism | 33 | 26 | 59 | 323 | 0.015 |
ko00561 | Glycerolipid metabolism | 18 | 15 | 33 | 171 | 0.029 |
ko00100 | Steroid biosynthesis | 8 | 4 | 12 | 49 | 0.032 |
ko00514 | Other types of O-glycan biosynthesis | 2 | 2 | 4 | 10 | 0.039 |
ko00040 | Pentose and glucuronate interconversions | 16 | 6 | 22 | 109 | 0.042 |
Pathway ID | Pathway | Up_Number | Down_Number | DEG_Number | Total_Number | p |
---|---|---|---|---|---|---|
ko04075 | Plant hormone signal transduction | 42 | 47 | 89 | 455 | 1.748 × 10−8 |
ko00906 | Carotenoid biosynthesis | 24 | 1 | 25 | 78 | 3.358 × 10−7 |
ko04016 | MAPK signaling pathway plant | 21 | 30 | 51 | 242 | 2.076 × 10−6 |
ko04712 | Circadian rhythm-plant | 29 | 3 | 32 | 126 | 2.896 × 10−6 |
ko00500 | Starch and sucrose metabolism | 40 | 24 | 64 | 333 | 3.199 × 10−6 |
ko00630 | Glyoxylate and dicarboxylate metabolism | 31 | 11 | 42 | 228 | 3.805 × 10−4 |
ko00260 | Glycine, serine and threonine metabolism | 24 | 11 | 35 | 185 | 6.814 × 10−4 |
ko00052 | Galactose metabolism | 15 | 13 | 28 | 138 | 7.346 × 10−4 |
ko00940 | Phenylpropanoid biosynthesis | 20 | 22 | 42 | 242 | 1.320 × 10−3 |
ko00909 | Sesquiterpenoid and triterpenoid biosynthesis | 12 | 1 | 13 | 51 | 2.425 × 10−3 |
ko00710 | Carbon fixation in photosynthetic organisms | 30 | 10 | 40 | 237 | 2.847 × 10−3 |
ko00942 | Anthocyanin biosynthesis | 3 | 0 | 3 | 6 | 0.020 |
ko00350 | Tyrosine metabolism | 5 | 13 | 18 | 102 | 0.025 |
ko02010 | ABC transporters | 13 | 7 | 20 | 117 | 0.025 |
ko00250 | Alanine, aspartate and glutamate metabolism | 6 | 15 | 21 | 125 | 0.027 |
ko00100 | Steroid biosynthesis | 7 | 3 | 10 | 49 | 0.034 |
ko00561 | Glycerolipid metabolism | 11 | 15 | 26 | 171 | 0.046 |
Pathway ID | Pathway | Up_Number | Down_Number | DEG_Number | Total_Number | p |
---|---|---|---|---|---|---|
ko04626 | Plant-pathogen interaction | 26 | 41 | 67 | 571 | 2.335 × 10−23 |
ko00380 | Tryptophan metabolism | 5 | 2 | 7 | 96 | 0.019 |
ko03410 | Base excision repair | 1 | 5 | 6 | 78 | 0.023 |
ko00330 | Arginine and proline metabolism | 7 | 2 | 9 | 156 | 0.034 |
ko00940 | Phenylpropanoid biosynthesis | 5 | 7 | 12 | 242 | 0.043 |
Pathway ID | Pathway | Up_Number | Down_Number | DEG_Number | Total_Number | p |
---|---|---|---|---|---|---|
ko04626 | Plant–pathogen interaction | 33 | 17 | 50 | 571 | 7.270 × 10−14 |
ko00940 | Phenylpropanoid biosynthesis | 6 | 11 | 17 | 242 | 2.300 × 10−4 |
ko00909 | Sesquiterpenoid and triterpenoid biosynthesis | 4 | 2 | 6 | 51 | 2.074 × 10−3 |
ko00270 | Cysteine and methionine metabolism | 7 | 5 | 12 | 247 | 0.030 |
Pathway ID | Pathway | Level2 | p |
---|---|---|---|
ko00240 | Pyrimidine metabolism | Nucleotide metabolism | 0.049 |
ko00520 | Amino sugar and nucleotide sugar metabolism | Carbohydrate metabolism | 0.051 |
ko00780 | Biotin metabolism | Metabolism of cofactors and vitamins | 0.094 |
ko00073 | Cutin, suberin and wax biosynthesis | Lipid metabolism | 0.094 |
ko00710 | Carbon fixation in photosynthetic organisms | Energy metabolism | 0.126 |
ko00620 | Pyruvate metabolism | Carbohydrate metabolism | 0.182 |
ko00906 | Carotenoid biosynthesis | Metabolism of terpenoids and polyketides | 0.184 |
ko04626 | Plant-pathogen interaction | Environmental adaptation | 0.184 |
ko00360 | Phenylalanine metabolism | Amino acid metabolism | 0.229 |
ko00130 | Ubiquinone and other terpenoid-quinone biosynthesis | Metabolism of cofactors and vitamins | 0.235 |
Pathway ID | Pathway | Level2 | p |
---|---|---|---|
ko00640 | Propanoate metabolism | Carbohydrate metabolism | 0.045 |
ko00630 | Glyoxylate and dicarboxylate metabolism | Carbohydrate metabolism | 0.080 |
ko00620 | Pyruvate metabolism | Carbohydrate metabolism | 0.104 |
ko00520 | Amino sugar and nucleotide sugar metabolism | Carbohydrate metabolism | 0.112 |
ko00010 | Glycolysis/Gluconeogenesis | Carbohydrate metabolism | 0.121 |
miRNA | Gene ID | Gene Annotation | QLCK vs. QLCT | RACK vs. RACT | ||
---|---|---|---|---|---|---|
log2FC of miRNA | log2FC of Gene | log2FC of miRNA | log2FC of Gene | |||
cal-miR396-17 | TRINITY_DN16498_c0_g1 | Unknown | 1.200 * | −0.898 | 0.139 | −1.557 * |
cal-miR1446-1 | TRINITY_DN881_c0_g1 | Unknown | −1.051 * | −1.179 * | 1.308 | −0.770 |
TRINITY_DN1114_c0_g1 | Heavy metal-associated isoprenylated plant protein 7 | −1.051 * | −0.671 | 1.308 | −1.356 * | |
cal-miR159-39 | TRINITY_DN76209_c0_g1 | Auxin response factor 2A | 0.615 | 2.002 * | 1.992 * | 0.981 |
cal-miR171_2-1 | TRINITY_DN10933_c0_g1 | Scarecrow-like protein 6 | 1.018 * | 1.771 * | −0.583 | 1.436 * |
cal-miR171_2-6 | TRINITY_DN2165_c0_g1 | Unknown | 2.825 * | 1.458 * | 0.596 | 1.309 * |
TRINITY_DN2165_c0_g2 | Scarecrow-like protein 6 | 2.825 * | 1.102 * | 0.596 | 1.081 * | |
cal-miR394-1 | TRINITY_DN18405_c0_g1 | U-box domain-containing protein | 1.687 * | 2.940 * | −0.308 | 0.869 |
cal-miR396-17 | TRINITY_DN4681_c0_g1 | Unknown | 1.200 * | 0.605 | 0.139 | 1.156 * |
TRINITY_DN1128_c2_g1 | Transketolase-2 | 1.226 * | 1.154 * | 0.139 | 1.137 * | |
cal-miR396-23 | TRINITY_DN1989_c0_g1 | Unknown | 0.032 | −3.022 * | 2.322 * | −1.548 * |
cal-miR397-3 | TRINITY_DN4966_c0_g1 | Laccase-4 | 4.368 * | 5.340 * | −0.581 | 2.559 |
TRINITY_DN24638_c0_g1 | Laccase-17 | 4.368 * | Inf * | −0.581 | 1.590 | |
TRINITY_DN4966_c0_g2 | Laccase-2 | 4.368 * | 7.229 * | −0.581 | 3.786 * | |
cal-miR398_2-3 | TRINITY_DN38515_c0_g1 | Unknown | −1.057 * | Inf * | 0.502 | Inf * |
cal-miR482-22 | TRINITY_DN23504_c1_g1 | Suppressor of npr1-1, constitutive 1 | −0.507 | −0.700 | 1.668 * | −3.987 * |
cal-undef-161 | TRINITY_DN5262_c0_g1 | 4-coumarate--CoA ligase 1 | −1.952 * | 1.636 * | −0.652 | 1.250 |
cal-undef-8 | TRINITY_DN5031_c0_g1 | Unknown | −1.471 | −3.372 * | −0.559 | −3.458 * |
TRINITY_DN6730_c0_g1 | E3 ubiquitin-protein ligase | −1.471 * | 1.160 * | −0.559 | 0.571 |
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Lai, R.; Guan, Q.; Shen, C.; Feng, X.; Zhang, Y.; Chen, Y.; Cheng, C.; Wu, R. Integrated SRNA-Seq and RNA-Seq Analysis Reveals the Regulatory Roles of miRNAs in the Low-Temperature Responses of Canarium album. Horticulturae 2022, 8, 667. https://doi.org/10.3390/horticulturae8070667
Lai R, Guan Q, Shen C, Feng X, Zhang Y, Chen Y, Cheng C, Wu R. Integrated SRNA-Seq and RNA-Seq Analysis Reveals the Regulatory Roles of miRNAs in the Low-Temperature Responses of Canarium album. Horticulturae. 2022; 8(7):667. https://doi.org/10.3390/horticulturae8070667
Chicago/Turabian StyleLai, Ruilian, Qingxu Guan, Chaogui Shen, Xin Feng, Yongyan Zhang, Yiting Chen, Chunzhen Cheng, and Rujian Wu. 2022. "Integrated SRNA-Seq and RNA-Seq Analysis Reveals the Regulatory Roles of miRNAs in the Low-Temperature Responses of Canarium album" Horticulturae 8, no. 7: 667. https://doi.org/10.3390/horticulturae8070667