Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing and Gene Structure Re-Annotation
2.2. The Identification of Differentially Expressed Genes
2.3. GO and KEGG Annotation of DEGs
2.4. The Change of Chloroplast- and Photosynthesis-Related Genes Expression
2.5. Silencing of Candidate Genes Altered Leaf Phenotypes of Mulberry
2.6. Gene Co-Expression and PPI Networks of Candidate Genes
3. Discussion
3.1. The Highly Quality Genes Annotation of Cultivated Mulberry (Morus alba)
3.2. Photosynthesis- and Chloroplast-Related DEGs Affect Photosynthesis to Further Change Biomass and Yield in Mulberry
3.3. Mulberry MaCLA1, MaTHIC, and MaPKP2 Regulatory Network
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Measurement of Net Photosynthetic Rate (Pn), Extraction of Transcriptomes, and Sequencing
4.3. Gene Structure and Transcriptome Mapping Re-Annotation
4.4. Differential Expression Analysis
4.5. GO and KEGG Enrichment Analysis
4.6. Virus-Induced Gene Silencing (VIGS) of Candidate Genes
4.7. Quantitative Reverse-Transcribed PCR (qRT-PCR) Analysis
4.8. Measurement of Chlorophyll Content
4.9. Analysis of Gene Co-Expression and PPI Networks
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Total Reads | Mapped Reads | Unique-Mapped Reads | Multi-Mapped Reads | Total Alignments (%) | Unique Alignments (%) | Multi Alignments (%) |
---|---|---|---|---|---|---|---|
E1-10-1 | 49904388 | 45571463 | 44143546 | 1427917 | 91.32 | 88.46 | 2.86 |
E1-10-2 | 56420992 | 51638586 | 49910614 | 1727972 | 91.52 | 88.46 | 3.06 |
E1-10-3 | 54262738 | 49480593 | 47802340 | 1678253 | 91.19 | 88.09 | 3.09 |
E1-12-1 | 59327236 | 54142095 | 52301878 | 1840217 | 91.26 | 88.16 | 3.1 |
E1-12-2 | 50923264 | 46383918 | 44886044 | 1497874 | 91.09 | 88.14 | 2.94 |
E1-12-3 | 56418276 | 51324742 | 49280862 | 2043880 | 90.97 | 87.35 | 3.62 |
E2-10-1 | 55613350 | 51299112 | 49545826 | 1753286 | 92.24 | 89.09 | 3.15 |
E2-10-2 | 47755332 | 43994904 | 42473230 | 1521674 | 92.13 | 88.94 | 3.19 |
E2-10-3 | 57610636 | 53335418 | 51765800 | 1569618 | 92.58 | 89.85 | 2.72 |
E2-12-1 | 53042616 | 48929692 | 46449439 | 2480253 | 92.25 | 87.57 | 4.68 |
E2-12-2 | 63794488 | 59118053 | 56404894 | 2713159 | 92.67 | 88.42 | 4.25 |
E2-12-3 | 51907882 | 47912048 | 45849994 | 2062054 | 92.3 | 88.33 | 3.97 |
H32-10-1 | 45519424 | 42730393 | 41251247 | 1479146 | 93.87 | 90.62 | 3.25 |
H32-10-2 | 53754266 | 50627556 | 48978022 | 1649534 | 94.18 | 91.11 | 3.07 |
H32-10-3 | 51907008 | 48613770 | 47046841 | 1566929 | 93.66 | 90.64 | 3.02 |
H32-12-1 | 53312124 | 50020860 | 48357132 | 1663728 | 93.83 | 90.71 | 3.12 |
H32-12-2 | 53322894 | 50059674 | 48425378 | 1634296 | 93.88 | 90.82 | 3.06 |
H32-12-3 | 57476448 | 53999036 | 52269167 | 1729869 | 93.95 | 90.94 | 3.01 |
Type | Morus alba |
---|---|
Number of genes | 22,664 |
Mean length of genomic loci | 3213 |
Mean exon number | 5.07 |
Mean CDS length | 1226 |
Genes with functional annotations | 20,185 |
Genes with GO terms | 12,438 |
Gene with ko terms | 10,379 |
Complete BUSCOs | 93.40% |
Fragmented BUSCOs | 4.20% |
Missing BUSCOs | 2.40% |
Gene_ID | At_Gene | Identify (%) | Gene_Name | Function |
---|---|---|---|---|
Moa12g01070.1 | AT2G37770.2 | 68.932 | ChlAKR | NAD(P)-linked oxidoreductase superfamily protein |
Moa02g03470.1 | AT4G15560.1 | 87.593 | CLA1 | Deoxyxylulose-5-phosphate synthase |
Moa02g13070.1 | AT1G15510.1 | 65.862 | ECB2 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa07g15800.1 | AT3G18110.1 | 75.309 | EMB1270 | Pentatricopeptide repeat (PPR) superfamily protein |
Moa11g02010.1 | AT3G49240.1 | 62.937 | emb1796 | Pentatricopeptide repeat (PPR) superfamily protein |
Moa12g01710.1 | AT3G54090.1 | 70.41 | FLN1 | fructokinase-like 1 |
Moa14g05970.1 | AT1G69200.1 | 63.729 | FLN2 | fructokinase-like 2 |
Moa02g05740.1 | AT3G23020.1 | 60.093 | PPR30 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa09g08310.1 | AT1G01320.2 | 60.808 | REC1 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa10g03540.1 | AT5G39980.1 | 83.251 | EMB3140 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa07g06690.1 | AT5G59200.1 | 64.516 | OTP80 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa06g09830.1 | AT2G29760.1 | 60.377 | OTP81 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa01g09900.1 | AT1G08070.1 | 66.584 | OTP82 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa04g00100.1 | AT3G57430.1 | 65.682 | OTP84 | Tetratricopeptide repeat (TPR)-like superfamily protein |
Moa14g04910.1 | AT2G02980.1 | 67.295 | OTP85 | Pentatricopeptide repeat (PPR) superfamily protein |
pgp033 | ATCG00730.1 | 98.758 | petD | photosynthetic electron transfer D |
Moa11g02720.1 | AT5G52920.1 | 84.974 | PKP-BETA1 | plastidic pyruvate kinase beta subunit 1 |
pgp064 | ATCG00350.1 | 97.867 | psaA | Photosystem I, PsaA/PsaB protein |
pgp065 | ATCG00340.1 | 97.684 | psaB | Photosystem I, PsaA/PsaB protein |
pgp038 | ATCG00680.1 | 97.441 | psbB | photosystem II reaction center protein B |
pgp068 | ATCG00280.1 | 97.674 | psbC | photosystem II reaction center protein C |
pgp080 | ATCG00080.1 | 100 | psbI | photosystem II reaction center protein I |
pgp067 | ATCG00300.1 | 91.935 | psbZ | YCF9 |
pgp056 | ATCG00490.1 | 94.737 | rbcL | ribulose-bisphosphate carboxylases |
pgp074 | ATCG00170.1 | 80.87 | rpoC2 | DNA-directed RNA polymerase family protein |
pgp031 | ATCG00750.1 | 92.754 | rps11 | ribosomal protein S11 |
Moa07g03450.1 | AT3G51895.1 | 76.888 | SULTR3:1 | sulfate transporter 3;1 |
Moa06g10020.1 | AT2G29630.3 | 86.574 | THIC | thiaminC |
Moa02g08320.1 | AT3G06730.1 | 78.621 | TRXz | Thioredoxin z |
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Li, Y.; Yu, C.; Mo, R.; Zhu, Z.; Dong, Z.; Hu, X.; Deng, W.; Zhuang, C. Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing. Int. J. Mol. Sci. 2022, 23, 8620. https://doi.org/10.3390/ijms23158620
Li Y, Yu C, Mo R, Zhu Z, Dong Z, Hu X, Deng W, Zhuang C. Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing. International Journal of Molecular Sciences. 2022; 23(15):8620. https://doi.org/10.3390/ijms23158620
Chicago/Turabian StyleLi, Yong, Cui Yu, Rongli Mo, Zhixian Zhu, Zhaoxia Dong, Xingming Hu, Wen Deng, and Chuxiong Zhuang. 2022. "Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing" International Journal of Molecular Sciences 23, no. 15: 8620. https://doi.org/10.3390/ijms23158620
APA StyleLi, Y., Yu, C., Mo, R., Zhu, Z., Dong, Z., Hu, X., Deng, W., & Zhuang, C. (2022). Screening and Verification of Photosynthesis and Chloroplast-Related Genes in Mulberry by Comparative RNA-Seq and Virus-Induced Gene Silencing. International Journal of Molecular Sciences, 23(15), 8620. https://doi.org/10.3390/ijms23158620