Chinese Bulletin of Botany ›› 2022, Vol. 57 ›› Issue (2): 182-196.DOI: 10.11983/CBB21189
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Haixia Xu, Jing He, Hang Yi, Li Wang(
)
HomeReceived:2021-11-08
Accepted:2022-02-25
Online:2022-03-01
Published:2022-03-24
Contact:
Li Wang
Haixia Xu, Jing He, Hang Yi, Li Wang. Sex Specific Response Mechanism of Transcriptome in Both Male and Female Marchantia polymorpha Under Cadmium Stress[J]. Chinese Bulletin of Botany, 2022, 57(2): 182-196.
| Gene names | Primer sequences (5'-3') |
|---|---|
| MpPCS | F: GAGTCCTTTCGAGCGAATTCT |
| R: AATCTTCCAGCAGTAGCAGTAG | |
| MpActin | F: AGGCATCTGGTATCCACGAG |
| R: ACATGGTCGTTCCTCCAGAC | |
| MARPO_0086s0070 | F: ATTGTCACTTCAAACTGCTTCC R: CTTTGCCAGTATGCTTTCAACT |
| MARPO_0265s0002 | F: TGGCGACTCTTAAAATAGCTCT R: GAAAGTATGGGATTCTTGCGAC |
| MARPO_0001s0061 | F: GAGGAAAATCAACGATACAGGC R: CTTCTCTTGCAGTCAGTTGTTC |
| MARPO_0145s0031 | F: CGTAGGGAGATCAGTGATTACC R: CCTTGTATAACTCACGATCGGA |
| MARPO_0003s0122 | F: TGGACAGAAAACTCATTGGTCT R: ACTTCCTTCTCTCTCACCAATG |
| MARPO_0003s0268 | F: GACTAGGGTTCCTTGGTTCTAC R: CATAATCGGGAAAACGTAACCC |
| MARPO_0011s0046 | F: CGGCTCAGATGTTGATAAATCA R: ATGCACTTCGCTGATCTCATAA |
| MARPO_0032s0085 | F: CCCCTCATCTCAAACTACTTGT R: TTGGAAAAGGAATTGCTGGATG |
Table 1 Primer sequences for qRT-PCR
| Gene names | Primer sequences (5'-3') |
|---|---|
| MpPCS | F: GAGTCCTTTCGAGCGAATTCT |
| R: AATCTTCCAGCAGTAGCAGTAG | |
| MpActin | F: AGGCATCTGGTATCCACGAG |
| R: ACATGGTCGTTCCTCCAGAC | |
| MARPO_0086s0070 | F: ATTGTCACTTCAAACTGCTTCC R: CTTTGCCAGTATGCTTTCAACT |
| MARPO_0265s0002 | F: TGGCGACTCTTAAAATAGCTCT R: GAAAGTATGGGATTCTTGCGAC |
| MARPO_0001s0061 | F: GAGGAAAATCAACGATACAGGC R: CTTCTCTTGCAGTCAGTTGTTC |
| MARPO_0145s0031 | F: CGTAGGGAGATCAGTGATTACC R: CCTTGTATAACTCACGATCGGA |
| MARPO_0003s0122 | F: TGGACAGAAAACTCATTGGTCT R: ACTTCCTTCTCTCTCACCAATG |
| MARPO_0003s0268 | F: GACTAGGGTTCCTTGGTTCTAC R: CATAATCGGGAAAACGTAACCC |
| MARPO_0011s0046 | F: CGGCTCAGATGTTGATAAATCA R: ATGCACTTCGCTGATCTCATAA |
| MARPO_0032s0085 | F: CCCCTCATCTCAAACTACTTGT R: TTGGAAAAGGAATTGCTGGATG |
Figure 1 Morphology of female (A) and male (B) Marchantia polymorpha after cadmium (Cd) treatment Five time points after Cd treatment: 0, 24, 48, 96 and 168 h. Bars=2 cm
| Sample_ID | Raw reads | Clean reads | Error (%) | Q20 (%) | Q30 (%) | GC (%) | Total mapped (%) |
|---|---|---|---|---|---|---|---|
| CK_F1 | 50740902 | 50191272 | 0.0241 | 98.38 | 95.02 | 50.92 | 94.74 |
| CK_F2 | 58049938 | 57506790 | 0.0242 | 98.36 | 94.95 | 50.98 | 89.75 |
| CK_F3 | 53602814 | 53058498 | 0.0245 | 98.23 | 94.63 | 51.23 | 95.59 |
| CK_M1 | 49826850 | 49313610 | 0.0243 | 98.31 | 94.84 | 51.14 | 94.22 |
| CK_M2 | 52605578 | 51996578 | 0.0245 | 98.25 | 94.67 | 51.13 | 91.95 |
| CK_M3 | 50064978 | 49523028 | 0.0242 | 98.36 | 94.96 | 50.94 | 90.51 |
| Cd_F1 | 53604084 | 53084914 | 0.0241 | 98.40 | 95.03 | 51.02 | 94.65 |
| Cd_F2 | 48343374 | 47896356 | 0.0255 | 97.87 | 93.60 | 50.53 | 95.16 |
| Cd_F3 | 48556392 | 48058072 | 0.0247 | 98.15 | 94.43 | 50.90 | 96.26 |
| Cd_M1 | 51066022 | 50567610 | 0.0244 | 98.28 | 94.75 | 50.66 | 87.88 |
| Cd_M2 | 51079094 | 50542790 | 0.0244 | 98.28 | 94.75 | 50.48 | 90.25 |
| Cd_M3 | 54825492 | 54241196 | 0.0249 | 98.06 | 94.19 | 50.61 | 93.78 |
Table 2 Transcriptome quality control data
| Sample_ID | Raw reads | Clean reads | Error (%) | Q20 (%) | Q30 (%) | GC (%) | Total mapped (%) |
|---|---|---|---|---|---|---|---|
| CK_F1 | 50740902 | 50191272 | 0.0241 | 98.38 | 95.02 | 50.92 | 94.74 |
| CK_F2 | 58049938 | 57506790 | 0.0242 | 98.36 | 94.95 | 50.98 | 89.75 |
| CK_F3 | 53602814 | 53058498 | 0.0245 | 98.23 | 94.63 | 51.23 | 95.59 |
| CK_M1 | 49826850 | 49313610 | 0.0243 | 98.31 | 94.84 | 51.14 | 94.22 |
| CK_M2 | 52605578 | 51996578 | 0.0245 | 98.25 | 94.67 | 51.13 | 91.95 |
| CK_M3 | 50064978 | 49523028 | 0.0242 | 98.36 | 94.96 | 50.94 | 90.51 |
| Cd_F1 | 53604084 | 53084914 | 0.0241 | 98.40 | 95.03 | 51.02 | 94.65 |
| Cd_F2 | 48343374 | 47896356 | 0.0255 | 97.87 | 93.60 | 50.53 | 95.16 |
| Cd_F3 | 48556392 | 48058072 | 0.0247 | 98.15 | 94.43 | 50.90 | 96.26 |
| Cd_M1 | 51066022 | 50567610 | 0.0244 | 98.28 | 94.75 | 50.66 | 87.88 |
| Cd_M2 | 51079094 | 50542790 | 0.0244 | 98.28 | 94.75 | 50.48 | 90.25 |
| Cd_M3 | 54825492 | 54241196 | 0.0249 | 98.06 | 94.19 | 50.61 | 93.78 |
Figure 2 Correlation analysis among female and male Marchantia polymorpha samples (A) Scatter plot of correlation about average level of gene expression and overall connectivity between female and male samples (females as x-axis and males as y-axis); (B) Clustered heatmap of correlation among samples
Figure 3 Statistics of differentially expressed genes between female and male Marchantia polymorpha in response to cadmium stress (A) Histograms of differentially expressed genes (DEGs); (B) Venn diagram of number of differential genes with different changing trends
Figure 4 Differentially expressed transcription factors between female and male Marchantia polymorpha in response to cadmium stress
Figure 5 Weighted gene co-expression network analysis of female and male Marchantia polymorpha response to cadmium stress (A) Cluster dendrogram of genes and modules; (B) Heatmap of correlation between modules and phenotypes. Red indicates positive correlation and blue indicates negative correlation.
Figure 6 Enrichment analysis of target modules (A) Top ten GO enrichment of salmon module; (B) Top ten GO enrichment of black module; (C) Top ten KEGG enrichment of salmon module; (D) Top ten KEGG enrichment of black module
Figure 7 Co-expression network diagram and hub genes of the salmon module and black module The diameter of dot from small to large, with light to dark colors represents the increasement in degree.
| Module | Gene names | Protein names |
|---|---|---|
| black | MARPO_0147s0038 | Phytocyanin domain-containing protein |
| black | MARPO_1326s0001 | ANK_REP_REGION domain-containing protein |
| black | MARPO_0015s0058 | NAC domain-containing protein |
| black | MARPO_0068s0011 | Hydrolase_4 domain-containing protein |
| black | MARPO_0034s0124 | Protein kinase domain-containing protein |
| salmon | MARPO_4159s0001 | Protein kinase domain-containing protein (fragment) |
| salmon | MARPO_0097s0006 | SCP domain-containing protein |
| salmon | MARPO_0047s0057 | FAD-binding FR-type domain-containing protein |
| salmon | MARPO_0009s0238 | S-protein homolog |
| salmon | MARPO_0047s0055 | FAD-binding FR-type domain-containing protein |
Table 3 Functional annotation of hub genes in salmon module and black module
| Module | Gene names | Protein names |
|---|---|---|
| black | MARPO_0147s0038 | Phytocyanin domain-containing protein |
| black | MARPO_1326s0001 | ANK_REP_REGION domain-containing protein |
| black | MARPO_0015s0058 | NAC domain-containing protein |
| black | MARPO_0068s0011 | Hydrolase_4 domain-containing protein |
| black | MARPO_0034s0124 | Protein kinase domain-containing protein |
| salmon | MARPO_4159s0001 | Protein kinase domain-containing protein (fragment) |
| salmon | MARPO_0097s0006 | SCP domain-containing protein |
| salmon | MARPO_0047s0057 | FAD-binding FR-type domain-containing protein |
| salmon | MARPO_0009s0238 | S-protein homolog |
| salmon | MARPO_0047s0055 | FAD-binding FR-type domain-containing protein |
Figure 8 Semi-quantitative analysis of gene expression and expression pattern validation (A) Semi-quantitative RT-PCR was used to detect transcription of marker genes (MpPCS) in four samples, 33 PCR cycles for MpPCS, 27 PCR cycles for MpAct (as an internal reference gene); (B) The expression data were verified by qRT-PCR
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