Insights into regulation of C2 and C4 photosynthesis in Amaranthaceae/Chenopodiaceae using RNA-Seq

Amaranthaceae (incl. Chenopodiaceae) show an immense diversity of C4 syndromes. More than 15 independent origins of C4 photosynthesis, partly in halophytic and/or succulent lineages, and the largest number of C4 species in eudicots signify the importance of this angiosperm lineage in C4 evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldiadiffusa (C3), Sedobassiasedoides (C2), and Bassiaprostrata (C4). Results show that B.prostrata belongs to the NADP–ME type and core genes encoding for C4 cycle are significantly up–regulated when compared to Sed.sedoides and T.diffusa, Sedobassiasedoides and B.prostrata share a number of up–regulated C4–related genes, however, two C4 transporters (DIT and TPT) are found significantly up–regulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C3 specific TFs is higher in C2 species as compared to C4 species, instead the C2 species show their own set of up–regulated TFs. Taken together, our study indicates that the hypothesis of the C2 photosynthesis as a proxy towards C4 photosynthesis is questionable in Sed.sedoides and more in favour of an independent evolutionary stable–state.

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Insights into Regulation of C2 and C4 Photosynthesis in Amaranthaceae/Chenopodiaceae Using RNA-Seq

International Journal of Molecular Sciences ◽

10.3390/ijms222212120 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12120

Author(s):

Christian Siadjeu ◽

Maximilian Lauterbach ◽

Gudrun Kadereit

Keyword(s):

Transcription Factors ◽

C4 Photosynthesis ◽

Stable State ◽

Comparative Transcriptome ◽

Rna Seq ◽

C4 Species ◽

Genes Encoding ◽

C4 Evolution ◽

Sedobassia Sedoides ◽

Core Genes

Amaranthaceae (incl. Chenopodiaceae) shows an immense diversity of C4 syndromes. More than 15 independent origins of C4 photosynthesis, and the largest number of C4 species in eudicots signify the importance of this angiosperm lineage in C4 evolution. Here, we conduct RNA-Seq followed by comparative transcriptome analysis of three species from Camphorosmeae representing related clades with different photosynthetic types: Threlkeldia diffusa (C3), Sedobassia sedoides (C2), and Bassia prostrata (C4). Results show that B. prostrata belongs to the NADP-ME type and core genes encoding for C4 cycle are significantly upregulated when compared with Sed. sedoides and T. diffusa. Sedobassia sedoides and B. prostrata share a number of upregulated C4-related genes; however, two C4 transporters (DIT and TPT) are found significantly upregulated only in Sed. sedoides. Combined analysis of transcription factors (TFs) of the closely related lineages (Camphorosmeae and Salsoleae) revealed that no C3-specific TFs are higher in C2 species compared with C4 species; instead, the C2 species show their own set of upregulated TFs. Taken together, our study indicates that the hypothesis of the C2 photosynthesis as a proxy towards C4 photosynthesis is questionable in Sed. sedoides and more in favour of an independent evolutionary stable state.

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Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome

Scientific Reports ◽

10.1038/s41598-020-74144-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Priya Singh ◽

Neeraj Bharti ◽

Amar Pal Singh ◽

Siddharth Kaushal Tripathi ◽

Saurabh Prakash Pandey ◽

...

Keyword(s):

Transcription Factors ◽

Large Scale ◽

Scale Up ◽

Differential Regulation ◽

Regulatory Proteins ◽

Comparative Transcriptome ◽

Ethylene Sensitivity ◽

Core Set ◽

Genes Encoding ◽

Rosa Bourboniana

Abstract Flowers of fragrant roses such as Rosa bourboniana are ethylene-sensitive and undergo rapid petal abscission while hybrid roses show reduced ethylene sensitivity and delayed abscission. To understand the molecular mechanism underlying these differences, a comparative transcriptome of petal abscission zones (AZ) of 0 h and 8 h ethylene-treated flowers from R. bourboniana was performed. Differential regulation of 3700 genes (1518 up, 2182 down) representing 8.5% of the AZ transcriptome was observed between 0 and 8 h ethylene-treated R. bourboniana petal AZ. Abscission was associated with large scale up-regulation of the ethylene pathway but prominent suppression of the JA, auxin and light-regulated pathways. Regulatory genes encoding kinases/phosphatases/F-box proteins and transcription factors formed the major group undergoing differential regulation besides genes for transporters, wall modification, defense and phenylpropanoid pathways. Further comparisons with ethylene-treated petals of R. bourboniana and 8 h ethylene-treated AZ (R. hybrida) identified a core set of 255 genes uniquely regulated by ethylene in R. bourboniana AZ. Almost 23% of these encoded regulatory proteins largely conserved with Arabidopsis AZ components. Most of these were up-regulated while an entire set of photosystem genes was prominently down-regulated. The studies provide important information on regulation of petal abscission in roses.

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Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq

PLoS ONE ◽

10.1371/journal.pone.0181061 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0181061 ◽

Cited By ~ 8

Author(s):

Chunbao Zhang ◽

Chunjing Lin ◽

Fuyou Fu ◽

Xiaofang Zhong ◽

Bao Peng ◽

...

Keyword(s):

Transcriptome Analysis ◽

F1 Hybrids ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis

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Comparative transcriptome analysis of transcription factors in different maize varieties under salt stress conditions

Plant Growth Regulation ◽

10.1007/s10725-016-0192-9 ◽

2016 ◽

Vol 81 (1) ◽

pp. 183-195 ◽

Cited By ~ 19

Author(s):

Xilong Du ◽

Gang Wang ◽

Jing Ji ◽

Liping Shi ◽

Chunfeng Guan ◽

...

Keyword(s):

Transcription Factors ◽

Salt Stress ◽

Transcriptome Analysis ◽

Stress Conditions ◽

Comparative Transcriptome ◽

Comparative Transcriptome Analysis ◽

Maize Varieties

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Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq

Molecular Genetics and Genomics ◽

10.1007/s00438-015-1041-7 ◽

2015 ◽

Vol 290 (5) ◽

pp. 1833-1847 ◽

Cited By ~ 10

Author(s):

Shengnan Huang ◽

Zhiyong Liu ◽

Runpeng Yao ◽

Danyang Li ◽

Hui Feng

Keyword(s):

Chinese Cabbage ◽

Transcriptome Analysis ◽

Brassica Campestris ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis ◽

Petal Degeneration Mutant

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Comparative transcriptome analysis of a fan-shaped inflorescence in pineapple using RNA-seq

Genomics ◽

10.1016/j.ygeno.2021.08.022 ◽

2021 ◽

Vol 113 (6) ◽

pp. 3653-3665

Author(s):

Tao Xie ◽

Jing Zhang ◽

Aiping Luan ◽

Wei Zhang ◽

Jing Wu ◽

...

Keyword(s):

Transcriptome Analysis ◽

Comparative Transcriptome ◽

Rna Seq ◽

Comparative Transcriptome Analysis

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Comparative Transcriptome Analysis Reveals the Potential Cardiovascular Protective Targets of the Thyroid Hormone Metabolite 3-Iodothyronamine (3-T1AM)

BioMed Research International ◽

10.1155/2020/1302453 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Zhou Haiyan ◽

Hu Bailong ◽

Zhang Bei ◽

Wang Yiming ◽

Liu Xingde

Keyword(s):

Cardiovascular Diseases ◽

Thyroid Hormone ◽

Transcriptome Analysis ◽

H9c2 Cells ◽

Comparative Transcriptome ◽

Rna Seq ◽

Hub Genes ◽

Comparative Transcriptome Analysis ◽

Protein Protein Interaction ◽

Protein Protein Interaction Networks

Background. The thyroid hormone metabolite 3-iodothyronamine (3-T1AM) is rapidly emerging as a promising compound in decreasing the heart rate and lowering the cardiac output. The aim of our study was to fully understand the molecular mechanism of 3-T1AM on cardiomyocytes and its potential targets in cardiovascular diseases. Materials and Methods. In our study, we utilized RNA-Seq to characterize the gene expression in H9C2 cells after 3-T1AM treatment. Comparative transcriptome analysis, including gene ontology, signaling pathways, disease connectivity analysis, and protein-protein interaction networks (PPI), was presented to find the critical gene function, hub genes, and related pathways. Results. A total of 1494 differently expressed genes (DEGs) were identified (192 upregulated and 1302 downregulated genes) in H9C2 cells for 3-T1AM treatment. Of these, 90 genes were associated with cardiovascular diseases. The PPI analysis indicated that 5 hub genes might be the targets of 3-T1AM. Subsequently, eight DEGs characterized using RNA-Seq were confirmed by RT-qPCR assays. Conclusions. Our study provides a comprehensive analysis of 3-T1AM on H9C2 cells and delineates a new insight into the therapeutic intervention of 3-T1AM for the cardiovascular diseases.

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