Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis)
Abstract
:1. Background
2. Results and Discussion
2.1. Transcriptome-Wide Detection of m6A Modification in Pak-choi
2.2. m6A Topological Patterns in Pak-choi
2.3. Differentially Expressed Genes Analysis
2.4. Association Analysis between Differentially Expressed Genes and Differential m6A Peaks
3. Materials and Methods
3.1. Plant Material and Tissue Collection
3.2. Library Construction and RNA Sequencing
3.3. Data Analysis
3.4. Biological Information Analysis
3.5. Expression and Function Analysis of Multilayer Genes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Availability of Data and Materials
Ethics Approval and Consent to Participate
Consent for Publication
Abbreviations
CDS | coding sequence |
FPKM | fragments per kilobase of exon model per million mapped reads |
GO | gene ontology |
HSP | heat stress protein |
KEGG | kyoto encyclopedia of genes and genomes |
m6A | N6-methyladenosine |
m6A-seq | RNA sequencing based on m6A RNA immunoprecipitation |
UTR | untranslated region |
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Sample | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Valid Bases | Q30 | GC |
---|---|---|---|---|---|---|---|
CK_1_input | 85.82 M | 12.92 G | 82.01 M | 9.07 G | 70.23% | 87.33% | 48.42% |
CK_1_IP | 80.33 M | 12.09 G | 76.98 M | 10.38 G | 85.82% | 87.88% | 47.28% |
CK_2_input | 86.32 M | 12.99 G | 83.84 M | 9.49 G | 73.04% | 87.36% | 48.52% |
CK_2_IP | 64.75 M | 9.71 G | 63.71 M | 8.38 G | 86.28% | 89.74% | 47.28% |
CK_3_input | 85.15 M | 12.82 G | 83.75 M | 9.59 G | 74.80% | 88.50% | 48.31% |
CK_3_IP | 73.17 M | 11.01 G | 69.33 M | 8.84 G | 80.32% | 87.21% | 46.96% |
T43_1_input | 80.40 M | 12.10 G | 78.73 M | 8.93 G | 73.79% | 88.72% | 48.16% |
T43_1_IP | 80.10 M | 12.01 G | 79.10 M | 9.40 G | 78.27% | 87.65% | 46.45% |
T43_2_input | 75.21 M | 11.28 G | 74.94 M | 8.54 G | 75.73% | 89.72% | 48.07% |
T43_2_IP | 77.01 M | 11.59 G | 73.52 M | 9.47 G | 81.67% | 88.03% | 46.85% |
T43_3_input | 85.14 M | 12.82 G | 81.97 M | 9.50 G | 74.11% | 87.03% | 48.03% |
T43_3_IP | 78.39 M | 11.80 G | 74.95 M | 9.48 G | 80.35% | 88.62% | 46.79% |
Sample | Total Reads | Total Mapped Reads | Multiple Mapped | Uniquely Mapped | Reads Mapped in Proper Pairs |
---|---|---|---|---|---|
CK_1_input | 82,012,256 | 72,759,712 (88.72%) | 4,178,829 (5.10%) | 68,580,883 (83.62%) | 66,920,836 (81.60%) |
CK_1_IP | 76,984,824 | 67,393,417 (87.54%) | 3,465,135 (4.50%) | 63,928,282 (83.04%) | 59,429,546 (77.20%) |
CK_2_input | 83,839,082 | 74,908,623 (89.35%) | 4,645,028 (5.54%) | 70,263,595 (83.81%) | 68,417,558 (81.61%) |
CK_2_IP | 63,714,740 | 56,726,613 (89.03%) | 3,176,962 (4.99%) | 53,549,651 (84.05%) | 50,426,514 (79.14%) |
CK_3_input | 83,747,818 | 75,954,376 (90.69%) | 4,321,180 (5.16%) | 71,633,196 (85.53%) | 69,931,644 (83.50%) |
CK_3_IP | 69,326,216 | 60,695,740 (87.55%) | 3,178,979 (4.59%) | 57,516,761 (82.97%) | 54,734,078 (78.95%) |
T43_1_input | 78,733,522 | 71,546,508 (90.87%) | 4,487,991 (5.70%) | 67,058,517 (85.17%) | 65,867,334 (83.66%) |
T43_1_IP | 79,099,558 | 69,007,966 (87.24%) | 4,462,602 (5.64%) | 64,545,364 (81.60%) | 61,905,290 (78.26%) |
T43_2_input | 74,935,246 | 68,759,115 (91.76%) | 4,272,256 (5.70%) | 64,486,859 (86.06%) | 63,435,032 (84.65%) |
T43_2_IP | 73,516,480 | 64,743,517 (88.07%) | 3,957,284 (5.38%) | 60,786,233 (82.68%) | 58,314,510 (79.32%) |
T43_3_input | 81,967,046 | 72,968,341 (89.02%) | 4,605,436 (5.62%) | 68,362,905 (83.40%) | 66,579,194 (81.23%) |
T43_3_IP | 74,954,614 | 66,014,828 (88.07%) | 4,025,106 (5.37%) | 61,989,722 (82.70%) | 59,600,270 (79.52%) |
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Liu, G.; Wang, J.; Hou, X. Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis). Plants 2020, 9, 1080. https://doi.org/10.3390/plants9091080
Liu G, Wang J, Hou X. Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis). Plants. 2020; 9(9):1080. https://doi.org/10.3390/plants9091080
Chicago/Turabian StyleLiu, Gaofeng, Jin Wang, and Xilin Hou. 2020. "Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis)" Plants 9, no. 9: 1080. https://doi.org/10.3390/plants9091080