Transcriptome Analysis Reveals Novel Insights into the Hyperaccumulator Phytolacca acinosa Roxb. Responses to Cadmium Stress
Abstract
:1. Introduction
2. Results
2.1. Response of P. acinosa Seeds to Cd2+ Treatment
2.2. Response of P. acinosa Seedlings to Cd2+ Treatment
2.3. P. acinosa Has a High Cd2+ Accumulation Capacity
2.4. De Novo Transcriptome Sequencing and Assembly
2.5. Functional Annotation of Unigenes
2.6. Differentially Expressed Genes (DEGs) Response to Cd2+ Stress in P. acinosa
2.7. GO Enrichment Analysis of DEGs
2.8. KEGG Pathway Enrichment Analysis of DEGs
2.9. Transcription Factors Were Differentially Expressed under Cd2+ Stress
2.10. Cell Wall-Related Genes Were Differentially Expressed under Cd2+ Stress
2.11. Secondary Metabolism-Related Genes Were Differentially Expressed under Cd2+ Stress
2.12. Membrane Proteins and Ion Transporters Were Differentially Expressed under Cd2+ Stress
2.13. Defense System-Related Genes Were Differentially Expressed under Cd2+ Stress
2.14. Validation of the DEGs by Real-Time PCR Analysis
3. Discussion
3.1. P. acinosa Can Be Used as a Candidate Plant for Cd Phytoremediation
3.2. Numerous TFs Were Involved in P. acinosa Response to Cd2+ Stress
3.3. Multiple Mechanisms Were Involved in Cd2+ Stress Tolerance in P. acinosa
3.4. ABC Transporters Were Involved in Regulating Cd2+ Stress
4. Materials and Methods
4.1. Materials and Cd2+ Treatment
4.2. Analysis of Seedling Traits
4.3. Cd2+ Content Analysis by ICP–MS
4.4. Measurement of MDA Content
4.5. Cd2+ Treatment for Transcriptome Sequencing
4.6. Library Preparation and Next Generation Sequencing
4.7. De Novo Transcriptome Assembly and Functional Annotation
4.8. Differentially Expression Analysis
4.9. Real-Time PCR Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Raw Reads Number | Raw Bases Number | Clean Reads Number | Clean Bases Number | Valid Bases (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|---|---|
CK1 | 34,397,898 | 5,159,684,700 | 34,004,184 | 5,075,043,936 | 98.35% | 98.57% | 95.56% | 44.00% |
CK2 | 42,980,760 | 6,447,114,000 | 42,566,702 | 6,353,506,726 | 98.54% | 98.65% | 95.74% | 44.00% |
CK3 | 43,298,432 | 6,494,764,800 | 42,821,964 | 6,391,566,154 | 98.41% | 98.63% | 95.67% | 44.00% |
Cd-T1 | 34,587,638 | 5,188,145,700 | 34,262,482 | 5,123,597,064 | 98.75% | 98.60% | 95.58% | 44.00% |
Cd-T2 | 38,393,362 | 4,759,004,300 | 38,182,134 | 4,682,860,231 | 98.40% | 98.57% | 95.55% | 44.00% |
Cd-T3 | 46,707,780 | 7,006,167,000 | 46,290,484 | 6,919,976,366 | 98.76% | 98.65% | 95.73% | 44.00% |
Type | Assembled Transcripts | Predicted Unigenes |
---|---|---|
Total sequence number | 255,468 | 124,408 |
Total sequence base | 299,181,020 | 113,753,609 |
Largest length (bp) | 17,759 | 17,759 |
Smallest length (bp) | 301 | 301 |
Average length (bp) | 1171.11 | 914.36 |
N50 length (bp) | 1781 | 1282 |
ID | Log2FC (Cd-T/CK) | Regulate | Annotation |
---|---|---|---|
cell wall biogenesis | |||
DN88120_c0_g1_i1 | −2.01 | Down | xyloglucan endotransglucosylase/hydrolase 2-like |
DN92891_c3_g4_i1 | 1.66 | Up | xyloglucan endotransglucosylase/hydrolase protein 23 |
DN92891_c3_g6_i1 | −2.72 | Down | xyloglucan endotransglucosylase/hydrolase protein22-like isoform X1 |
DN95917_c1_g1_i1 | −2.41 | Down | xyloglucan endotransglucosylase/hydrolase protein 23 |
DN96589_c1_g1_i2 | 2.41 | Up | xyloglucan endotransglucosylase/hydrolase protein 6 |
DN96589_c1_g5_i1 | −1.62 | Down | xyloglucan endotransglucosylase/hydrolase protein 6 |
DN97081_c2_g1_i11 | −1.21 | Down | beta-arabinofuranosyltransferase RAY1 isoform X3 |
DN97099_c2_g1_i1 | −1.47 | Down | xyloglucan endotransglucosylase/hydrolase protein 7 |
DN98746_c2_g1_i4 | −1.46 | Down | xyloglucan endotransglucosylase/hydrolase 3 |
DN99640_c5_g1_i1 | −1.05 | Down | hypothetical protein SOVF_125280 |
DN88120_c0_g2_i1 | −1.58 | Down | hypothetical protein SOVF_073730 |
cell wall organization | |||
DN100083_c6_g2_i4 | −1.11 | Down | hypothetical protein SOVF_144400 |
DN108829_c0_g1_i1 | 1.62 | Up | beta-1,3-galactosyltransferase 6 |
DN89571_c0_g1_i2 | 2.11 | Up | rhamnogalacturonate lyase B |
DN91042_c0_g1_i1 | 1.52 | Up | polygalacturonase-like |
DN91881_c0_g1_i1 | −1.66 | Down | hypothetical protein SOVF_175910 |
DN95973_c4_g1_i3 | −1.26 | Down | glucan endo-1,3-beta-glucosidase 13 |
DN95989_c1_g3_i3 | 1.28 | Up | NAC transcription factor |
DN96070_c1_g1_i10 | 1.97 | Up | hypothetical protein BVRB_5g098360 isoform B |
DN96441_c2_g2_i2 | −1.32 | Down | omega-hydroxypalmitate O-feruloyl transferase |
DN96517_c3_g4_i1 | −6.13 | Down | Putative UDP-glucuronate:xylan alpha-glucuronosyltransferase 4 |
DN96603_c7_g3_i1 | −2.65 | Down | hypothetical protein BVRB_9g215820 |
DN96627_c2_g1_i1 | −2.86 | Down | hypothetical protein BVRB_9g215820 |
DN97041_c1_g1_i1 | −1.09 | Down | leucine-rich repeat extensin-like protein 4 |
DN98038_c4_g1_i5 | −1.03 | Down | beta-1,4-xylosyltransferase IRX9 |
DN91881_c0_g2_i1 | −2.95 | Down | casparian strip membrane protein 3 |
DN92988_c2_g2_i1 | −1.20 | Down | GATA transcription factor 12 |
DN92954_c10_g1_i1 | −1.18 | Down | uncharacterized protein LOC104819621 |
cell wall modification | |||
DN92674_c4_g1_i2 | −1.39 | Down | pectinesterase/pectinesterase inhibitor 21 |
DN92816_c2_g3_i2 | −5.14 | Down | pectinesterase/pectinesterase inhibitor 59 |
DN94343_c1_g1_i1 | 1.25 | Up | KMT00424|hypothetical protein BVRB_9g217270 |
DN94343_c1_g2_i1 | 2.30 | Up | putative pectinesterase 11 |
DN99628_c2_g1_i2 | −1.35 | Down | casparian strip membrane protein 2 |
DN88314_c0_g1_i1 | −2.32 | Down | pectinesterase/pectinesterase inhibitor 12 |
cellulose biosynthetic process | |||
DN94431_c0_g5_i2 | 1.95 | Up | cellulose synthase-like protein G2 |
DN94789_c0_g4_i1 | −5.27 | Down | protein trichome birefringence-like 42 |
DN96659_c4_g1_i6 | 1.02 | Up | hypothetical protein SOVF_137370 |
DN98575_c9_g1_i2 | 1.16 | Up | hypothetical protein SOVF_143010 |
DN99723_c4_g4_i4 | −1.43 | Down | protein trichome birefringence-like 3 |
DN94431_c0_g6_i2 | 1.67 | Up | hypothetical protein SOVF_076670 |
DN97763_c1_g5_i1 | 1.13 | Up | hypothetical protein BVRB_5g111110 |
DN100016_c2_g3_i2 | 1.52 | Up | hypothetical protein BVRB_6g142540 |
DN100016_c2_g2_i1 | 3.83 | Up | hypothetical protein BVRB_6g142540 |
cellulose catabolic process | |||
DN94190_c4_g2_i1 | −1.28 | Down | endoglucanase 11 |
DN95890_c3_g1_i4 | −1.23 | Down | endoglucanase 6 |
DN96141_c3_g1_i4 | 1.19 | Up | uncharacterized protein LOC104893418 |
DN95568_c3_g5_i1 | −1.87 | Down | endoglucanase 12 |
DN86253_c0_g1_i1 | −2.54 | Down | hypothetical protein SOVF_009160 |
ID | Log2FC (Cd-T/CK) | Regulate | Annotation |
---|---|---|---|
Flavonoid biosynthesis | |||
DN110312_c0_g1_i1 | −3.55 | Down | chalcone synthase 2-like |
DN91008_c0_g1_i2 | −1.63 | Down | protein SRG1-like |
DN92655_c9_g1_i4 | 1.39 | Up | hypothetical protein SOVF_156310 |
DN92655_c9_g6_i1 | 1.32 | Up | hypothetical protein SOVF_156310 |
DN93138_c8_g4_i2 | 1.78 | Up | hypothetical protein SOVF_168370 |
DN93301_c1_g1_i3 | −2.93 | Down | chalcone synthase 2-like |
DN93562_c6_g3_i1 | 1.83 | Up | chalcone synthase |
DN95283_c6_g3_i1 | 1.53 | Up | hypothetical protein SOVF_192090 |
DN95456_c3_g5_i1 | 6.37 | Up | unnamed protein product |
DN95974_c2_g2_i1 | 1.55 | Up | hypothetical protein SOVF_200110 |
DN96124_c1_g1_i1 | −1.15 | Down | UDP-glycosyltransferase 79B6-like |
DN96124_c1_g6_i2 | 1.60 | Up | hypothetical protein SOVF_025340 |
DN96124_c1_g7_i2 | 1.28 | Up | hypothetical protein SOVF_025340 |
DN96763_c2_g1_i1 | 2.09 | Up | chalcone synthase |
DN99228_c1_g1_i1 | 1.55 | Up | flavanone-3-hydroxylase |
DN99283_c4_g1_i1 | −1.82 | Down | hypothetical protein SOVF_168360 |
phenylpropanoid biosynthesis | |||
DN94161_c5_g1_i3 | 1.19 | Up | cinnamyl alcohol dehydrogenase 1 |
DN98963_c5_g4_i1 | −2.27 | Down | hypothetical protein BVRB_8g195860 isoform B |
DN74041_c0_g1_i1 | −6.91 | Down | class III peroxidase |
DN86278_c0_g1_i1 | 4.72 | Up | peroxidase 4 |
DN93922_c5_g2_i1 | 4.30 | Up | hypothetical protein PRUPE_6G205600 |
DN96687_c1_g3_i2 | 1.06 | Up | phenylalanine ammonia-lyase, partial |
DN98188_c1_g4_i4 | 1.07 | Up | phenylalanine ammonia-lyase |
DN98963_c5_g4_i1 | −2.27 | Down | hypothetical protein BVRB_8g195860 isoform B |
Monoterpenoid biosynthesis | |||
DN93319_c3_g1_i1 | 1.81 | Up | (+)-neomenthol dehydrogenase-like, partial |
DN96631_c4_g3_i1 | 2.21 | Up | (+)-neomenthol dehydrogenase isoform X2 |
Cutin, suberine and wax biosynthesis | |||
DN96918_c3_g5_i1 | 2.40 | Up | hypothetical protein SOVF_091970 |
DN93789_c3_g1_i1 | −1.67 | Down | long chain acyl-CoA synthetase 1 |
DN95362_c6_g2_i1 | −2.06 | Down | hypothetical protein BVRB_1g012280 |
DN99249_c1_g1_i1 | 2.44 | Up | protein ECERIFERUM 3 |
DN99249_c1_g3_i4 | 3.35 | Up | protein ECERIFERUM 3 |
DN98976_c3_g1_i1 | −4.86 | Down | omega-hydroxypalmitate O-feruloyl transferase |
carotenoid biosynthesis | |||
DN98063_c4_g3_i1 | 1.04 | Up | cyclo-DOPA 5-O-glucosyltransferase |
DN20061_c0_g1_i1 | 2.16 | Up | 9-cis-epoxycarotenoid dioxygenase NCED5, chloroplastic |
Tropane, piperidine and pyridine alkaloid biosynthesis | |||
DN98183_c5_g1_i1 | 1.22 | Up | hypothetical protein SOVF_178490 isoform A |
ID | Primer Sequences 5′-3′ |
---|---|
DN92930_c2_g1_i1 | F: CCCTTTCACCCAGCCTAGTT |
R: TTGTACCAACGCCCCAAAGA | |
DN100451_c6_g2_i1 | F: TGGCTTCATGACAATCCGCT |
R: AACGGAAGCCTAACCACTCG | |
DN97551_c2_g1_i1 | F: GCGTGGACGGTATATGGGTT |
R: GCTACTGGCCCCATGAAGTT | |
DN99005_c3_g2_i1 | F: TGCAACCGTAAGCGGATACT |
R: ATCCCCTCTAAACCCGTCCA | |
DN99585_c3_g1_i2 | F: TTGCAGCCGCTTTCTATGGT |
R: GCCCTCTTCTGGTATGTGGG | |
DN95604_c7_g2_i2 | F: TCATGTTGGCTTGTGCTGGA |
R: AGTTGAGCGCACAGGATTGA | |
DN97835_c5_g5_i1 | F: AGAATGCGAAAGGCTTGGGA |
R: TGTGCTTGGTCCACACTCAG | |
DN97835_c5_g7_i3 | F: GTAACCTGGGTCATCGGCTC |
R: TGGCTGCAATCGCATACCTT | |
DN96587_c3_g1_i2 | F: AGTGTGGGGAGCCTAGTGAT |
R: GGTCTAAAGGACCCACACG | |
DN97830_c6_g5_i4 | F: GTAACACCTCCATCTCCGCC |
R: AAAAGCCACCGGAAGAAGC | |
DN89582_c0_g1_i1 | F: CCGAGACCCGTGTTTGTGTA |
R: CTGTTTTGGGCTTCACCAGC | |
DN95554_c2_g4_i1 | F: TGTGGCCCACTCAACTAAGG |
R: AGATCCCCACCTGGATCAGA | |
Actin | F: TTGAGCAGGAATCGGAG |
R: TGCTGCTTCCATACCTATC |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Xie, Q.; Deng, W.; Su, Y.; Ma, L.; Yang, H.; Yao, F.; Lin, W. Transcriptome Analysis Reveals Novel Insights into the Hyperaccumulator Phytolacca acinosa Roxb. Responses to Cadmium Stress. Plants 2024, 13, 297. https://doi.org/10.3390/plants13020297
Xie Q, Deng W, Su Y, Ma L, Yang H, Yao F, Lin W. Transcriptome Analysis Reveals Novel Insights into the Hyperaccumulator Phytolacca acinosa Roxb. Responses to Cadmium Stress. Plants. 2024; 13(2):297. https://doi.org/10.3390/plants13020297
Chicago/Turabian StyleXie, Qin, Wentao Deng, Yi Su, Liying Ma, Haijun Yang, Feihong Yao, and Wanhuang Lin. 2024. "Transcriptome Analysis Reveals Novel Insights into the Hyperaccumulator Phytolacca acinosa Roxb. Responses to Cadmium Stress" Plants 13, no. 2: 297. https://doi.org/10.3390/plants13020297