Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq
Abstract
:1. Introduction
2. Results
2.1. Descriptive Statistics of RNA Data and De Novo Assembly
2.2. Differential Expression Genes (DEGs) within Camphorosmeae
2.3. Functional Classification and Enrichment of DEGs within the Camphorosmeae
2.4. Differential Expression of C4-Related Genes in C3, C2 and C4 Camphorosmeae Species
2.5. Differential Expression of Key Photorespiration Genes in C3, C2 and C4 Camphorosmeae Species
2.6. Regulatory Elements in C3, C2, and C4 Species of the Amaranthaceae/Chenopodiaceae Alliance
3. Discussion
3.1. Transcriptome Analysis in Camphorosmeae
3.2. C4 Key Enzymes in C4 and C2 Camphorosmeae Species
3.3. C4 Key Enzymes in C4 and C2 Camphorosmeae Species
3.4. Regulation of C3, C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae
4. Materials and Methods
4.1. Plant Material
4.2. RNA Isolation and Sequencing
4.3. Data Access
4.4. RNA-Seq Data Processing
4.5. Differential Gene Expression Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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C2 vs. C4* | C3 vs. C4* | C3 vs. C2* | |||||
---|---|---|---|---|---|---|---|
Transcripts | Genes | Log2FC | Padj | Log2FC | P | Log2FC | Padj |
Bv_006710_gkqg.t1 | MDH | 1.29 | 1.01 × 10−10 | 2.84 | 9.92 × 10−42 | 1.55 | 1.74 × 10−14 |
Bv1_004490_tyfq.t1 | PHT4 | 1.57 | 1.56 × 10−11 | 2.89 | 1.72 × 10−31 | 1.32 | 7.56 × 10−08 |
Bv1_013550_fjqs.t1 | PPdK | 3.37 | 2.32 × 10−54 | 4.63 | 2.78 × 10−90 | 1.26 | 8.92 × 10−10 |
Bv2_031080_twkf.t1 | AspAt | 1.32 | 2.84 × 10−06 | 2.15 | 1.44 × 10−13 | 0.82 | 0.003667 |
Bv3_049110_qgnh.t1 | PHT1 | 3.16 | 8.05 × 10−08 | - | - | - | - |
Bv4_072630_xjai.t1 | DIT | - | - | 1.30 | 4.88 × 10−06 | 2.61 | 3.46 × 10−19 |
Bv5_117240_yhsk.t1 | PPT | 1.94 | 7.13 × 10−13 | 3.61 | 5.61 × 10−35 | 1.67 | 2.18 × 10−09 |
Bv6_135140_uyxu.t1 | Asn Synthetase | 2.56 | 5.60 × 10−07 | 2.42 | 1.93 × 10−06 | - | - |
Bv6_148840_uffy.t1 | CA | 3.80 | 6.66 × 10−38 | 3.81 | 4.08 × 10−38 | - | - |
Bv7_169130_kwer.t1 | AlaAT | 2.61 | 4.89 × 10−17 | 5.17 | 4.74 × 10−48 | 2.56 | 2.34 × 10−15 |
Bv8_182550_kstq.t1 | TPT | - | - | 1.48 | 1.20 × 10−10 | 2.29 | 2.71 × 10−22 |
Bv8_194450_rkme.t1 | CA | - | - | - | - | 1.48 | 0.000263 |
Bv8_195530_sxjq.t1 | BASS2 | 3.51 | 5.00 × 10−68 | 3.97 | 6.26 × 10−83 | 0.46 | 0.018625 |
Bv8_200290_ujgk.t1 | TPT | 3.25 | 1.25 × 10−05 | 1.97 | 0.005513 | ||
Bv9_209750_xeaz.t1 | PEPC | 2.95 | 3.29 × 10−17 | 4.12 | 6.98 × 10−29 | 1.18 | 0.000429 |
Bv9_215520_prze.t1 | DIT | 1.48 | 1.23 × 10−08 | 2.63 | 5.15 × 10−22 | 1.16 | 2.27 × 10−05 |
Bv9_224000_xpgi.t1 | NHD | 2.48 | 1.17 × 10−21 | 2.68 | 7.04 × 10−25 | - | - |
Bv9_224840_zmjw.t1 | NADP-ME | 1.29 | 8.44 × 10−08 | 3.86 | 9.54 × 10−47 | 2.56 | 1.34 × 10−23 |
C2* vs. C4 | C3 vs. C2* | C3* vs. C4 | |||||
---|---|---|---|---|---|---|---|
Transcripts | Genes | Log2FC | Padj | Log2FC | Padj | Log2FC | Padj |
Bv5_106360_ipey.t1 | GDC-H | 1.862968 | 3.37 × 10−15 | 0.990549 | 1.80 × 10−05 | 0.872432 | 0.000167 |
Bv_012000_yknj.t1 | GDC-P | 1.253616 | 9.20 × 10−08 | - | - | 2.068131 | 5.39 × 10−18 |
Bv3_059720_tshd.t1 | GDC-L | 1.281024 | 1.13 × 10−11 | - | - | 0.953812 | 3.95 × 10−07 |
Bv3_065510_eeis.t1 | SHMT | - | - | 1.133566 | 0.000228 | - | - |
Bv4_073470_iswc.t1 | AGT/SGT | 1.254967 | 2.18 × 10−07 | - | - | 1.130439 | 2.83 × 10−06 |
Bv4_074740_miaa.t1 | PGP | 1.831751 | 1.99 × 10−16 | 0.505181 | 0.019216 | 1.326602 | 1.77 × 10−09 |
Bv4_094290_jgpp.t1 | GOX | 1.708751 | 1.51 × 10−18 | 0.993515 | 1.94 × 10−07 | 0.715241 | 0.000175 |
Bv5_107350_ydma.t1 | 2.435018 | 1.25 × 10−13 | - | - | 2.32744 | 1.09 × 10−12 | |
Bv6_127540_qdph.t1 | GDC-T | 2.464812 | 2.21 × 10−23 | 1.030248 | 1.32 × 10−05 | 1.434602 | 2.66 × 10−09 |
Bv6_148110_nuir.t1 | GGT | 2.380809 | 3.21 × 10−21 | 1.223501 | 4.63 × 10−07 | 1.157324 | 2.02 × 10−06 |
Bv6_152820_wtfn.t1 | SHMT | 1.721992 | 2.64 × 10−18 | 0.734934 | 0.000137 | 0.987067 | 3.75 × 10−07 |
Bv8_184280_guso.t1 | 0.677745 | 0.006074 | - | - | 1.06935 | 3.85 × 10−06 | |
Bv9_213980_zwen.t1 | HPR | 0.96884 | 0.000282 | - | - | 0.531187 | 0.045313 |
Bv9_220360_xogt.t2 | GLYK | 0.689722 | 0.001207 | 0.708265 | 0.000885 | - | - |
Cluster-4 | |||||||||
---|---|---|---|---|---|---|---|---|---|
BBX15 (CO-Like) | SHR (GRAS) | SCZ (HSF) | LBD41 (LBD) | ||||||
Lineage | Species (C3 vs. C4*) | LF2C | Padj | LF2C | Padj | LF2C | Padj | LF2C | Padj |
Salsoleae | Salweb vs. Hsco | 8.8 | 3.84 × 10−24 | 2.23 | 1.55 × 10−08 | 5.59 | 1.73 × 10−05 | 3.71 | 6.05 × 10−13 |
Salweb vs. Salopp | 11.86 | 6.56 × 10−61 | 1.95 | 2.56 × 10−06 | 5.09 | 0.000374 | 4.26 | 1.64 × 10−17 | |
Salweb vs. Salsod | 11.57 | 6.71 × 10−62 | 2.63 | 1.85 × 10−13 | 7.66 | 4.94 × 10−20 | 2.84 | 2.06 × 10−07 | |
Camphorosmeae | Tdif vs. Bpro | 10.99 | 3.77 × 10−51 | 4.21 | 9.49 × 10−12 | 3.4 | 2.71 × 10−06 | 6.71 | 5.11 × 10−10 |
Salweb vs. Bpro | 10.82 | 2.50 × 10−47 | 1.45 | 0.0011 | 6.12 | 1.58 × 10−07 | 2.22 | 0.00019 | |
Salso. × Camph. | Tdif vs. Hsco | 8.96 | 2.75 × 10−27 | 4.99 | 2.89 × 10−19 | 2.84 | 0.000272 | 8.23 | 1.45 × 10−21 |
Tdif vs. Salsod | 11.72 | 1.85 × 10−63 | 5.34 | 5.60 × 10−25 | 5.25 | 3.76 × 10−21 | 6.96 | 1.91 × 10−12 | |
Tdif vs. Salopp | 12.03 | 6.61 × 10−65 | 4.7 | 1.56 × 10−15 | 2.44 | 0.00602 | 8.68 | 3.84 × 10−26 |
Cluster-9 | Cluster-10 | ||||||
---|---|---|---|---|---|---|---|
ATHB13 (HD-ZIP) | HSFA6B (HSF) | NAC083 (NAC) | |||||
Lineage | Species (C4 vs. C3*) | LF2C | Padj | LF2C | Padj | LF2C | Padj |
Salsoleae | Hsco vs. Salweb | 9.02 | 5.45 × 10−24 | 1.21 | 0.00017 | 0.73 | 0.00398 |
Salopp vs. Salweb | 1.71 | 2.77 × 10−05 | 1.54 | 1.32 × 10−05 | 1.42 | 4.44 × 10−08 | |
Salsod vs. Salweb | 1.14 | 0.00077 | 1.43 | 1.65 × 10−06 | 0.76 | 0.0004 | |
Camphorosmeae | Bpro vs. Tdif | 8.89 | 2.80 × 10−23 | 1.7 | 1.08 × 10−06 | 11.74 | 3.28 × 10−82 |
Bpro vs. Salweb | 8.99 | 8.45 × 10−24 | 1.91 | 5.76 × 10−08 | 11.28 | 1.31 × 10−72 | |
Salso. × Camph. | Hsco vs. Tdif | 8.92 | 1.78 × 10−23 | 1 | 0.00169 | 1.01 | 5.11 × 10−05 |
Salsod vs. Tdif | 0.87 | 0.00956 | 1.23 | 4.09 × 10−05 | 1.04 | 6.71 × 10−07 | |
Salopp vs. Tdif | 1.45 | 0.00038 | 1.34 | 0.00011 | 1.71 | 4.00 × 10−11 |
Cluster-2 | |||
---|---|---|---|
bHLH106 (bHLH) | |||
Lineage | Species (C3 vs. C2*) | LF2C | Padj |
Salsoleae | Sweb vs. Saldi1 | 1.68 | 8.90 × 10−13 |
Sweb vs. Saldi2 | 1.63 | 4.07 × 10−11 | |
Camphorosmeae | Tdif vs. Sedsed | 0.45 | 0.04616 |
Salso. × Camph. | Tdif vs. Sdi1 | 1.06 | 3.33 × 10−07 |
Tdif vs. Sdi2 | 1.01 | 2.79 × 10−06 | |
Sweb vs. Sedsed | 1.07 | 4.19 × 10−05 | |
Species (C4 vs. C2*) | LF2C | Padj | |
Salsoleae | Hsco vs. Saldi1 | 1.37 | 1.23 × 10−10 |
Hsco vs. Saldi 2 | 1.32 | 3.58 × 10−09 | |
Salopp vs. Saldi1 | 2.17 | 7.37 × 10−19 | |
Salopp vs. Saldi2 | 2.12 | 1.03 × 10−16 | |
Salsod vs. Saldi1 | 1.21 | 3.24 × 10−10 | |
Salsod vs. Saldi2 | 1.16 | 7.30 × 10−09 | |
Camphorosmeae | Bpro vs. Sedsed | 0.56 | 0.01398 |
Salso. × Camph. | Bpro vs. Saldi1 | 1.17 | 2.14 × 10−08 |
Bpro vs. Saldi2 | 1.12 | 2.21 × 10−07 | |
Hsco vs. Sedsed | 0.76 | 0.001176 | |
Salopp vs. Sedsed | 1.56 | 9.00 × 10−09 | |
Salsod vs. Sedsed | 0.6 | 0.00483 |
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Siadjeu, C.; Lauterbach, M.; Kadereit, G. Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq. Int. J. Mol. Sci. 2021, 22, 12120. https://doi.org/10.3390/ijms222212120
Siadjeu C, Lauterbach M, Kadereit G. Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq. International Journal of Molecular Sciences. 2021; 22(22):12120. https://doi.org/10.3390/ijms222212120
Chicago/Turabian StyleSiadjeu, Christian, Maximilian Lauterbach, and Gudrun Kadereit. 2021. "Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq" International Journal of Molecular Sciences 22, no. 22: 12120. https://doi.org/10.3390/ijms222212120