Transcriptome analysis of diploid and triploid <i>Populus tomentosa</i>

Wen, Bin; Liu, Xiaozhen; Zhang, Zhiming; Zhang, Hanyao

doi:10.7717/peerj.10204

Cited by 4 publications

(3 citation statements)

References 49 publications

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“…At the same leaf position, genes related to photosynthesis-and chlorophyll-related processes were upregulated in triploid populus. Similarly, genes related to the synthesis and transduction of hormones, such as auxin, mitogen, and brassinolide, were also upregulated, which led to speculation that the molecular mechanism that enhances photosynthesis and possible synthesis and transduction of plant hormones was the reason for its fast growth [16][17][18]. Liao et al [19] also found that after chromosome doubling, hormones such as auxin, CK, and GA increased in populus.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L.

Wu,

Guo,

Long

et al. 2024

IJMS

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Polyploid breeding techniques aid in the cultivation of new forestry cultivars, thus expanding the suite of strategies for the improvement of arboreal traits and innovation within the field of forestry. Compared to diploid Robinia pseudoacacia L. (black locust) ‘D26-5①’ (2×), its dwarfed homologous tetraploid ‘D26-5②’ (4×) variety has better application prospects in garden vegetation guardrails and urban landscape. However, the molecular mechanism of the generation and growth of this dwarf variety is still unclear. Here, plant growth and development as well as histological differences between the diploid and its autotetraploid were investigated. Levels of endogenous hormones at three different developmental stages (20, 40, and 70 days) of 2× and homologous 4× tissue culture plantlets were assessed, and it was found that the brassinosteroid (BR) contents of the former were significantly higher than the latter. Transcriptome sequencing data analysis of 2× and homologous 4× showed that differentially expressed genes (DEGs) were significantly enriched in plant hormone synthesis and signal transduction, sugar and starch metabolism, and the plant circadian rhythm pathway, which are closely related to plant growth and development. Therefore, these biological pathways may be important regulatory pathways leading to dwarfism and slow growth in tetraploids. Additionally, utilizing weighted gene coexpression network analysis (WGCNA), we identified three crucial differentially expressed genes (DEGs)—PRR5, CYP450, and SPA1—that potentially underlie the observed ploidy variation. This study provides a new reference for the molecular mechanism of dwarfism in dwarfed autotetraploid black locusts. Collectively, our results of metabolite analysis and comparative transcriptomics confirm that plant hormone signaling and the circadian rhythm pathway result in dwarfism in black locusts.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L.

Wu,

Guo,

Long

et al. 2024

IJMS

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“…Triploid Chinese white poplar ( P. tomentosa Carr., Salicaceae ) has stronger advantages in growth and better stress resistance and wood quality than diploid P. tomentosa . The expression levels of CYCD3 in triploid P. tomentosa are higher than those in diploid P. tomentosa 61 . Transgenic PtoCYCD3;3 makes poplar leaves large and curled, increases plant height and stem diameter 12 .…”

Section: Discussionmentioning

confidence: 77%

Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level

Liang

et al. 2022

Sci Rep

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Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1–D7) and 7 (CDKA–CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.

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“…PRJNA786265). Transcriptome assembly, sequence alignment, gene orthology determination, and gene set enrichment analysis were performed according to the method described by Bian [ 21 ]. Differential gene expression heat maps were plotted using Log2 (Fragments Per Kilobase of Exon Model per Million Mapped Fragments (FPKM) + 1) values with the R 3.0.2 software.…”

Section: Methodsmentioning

confidence: 99%

Overexpression of MET4 Leads to the Upregulation of Stress-Related Genes and Enhanced Sulfite Tolerance in Saccharomyces uvarum

Zhuo

Zhang

Zhao

et al. 2022

Cells

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Saccharomyces uvarum is one of the few fermentative species that can be used in winemaking, but its weak sulfite tolerance is the main reason for its further use. Previous studies have shown that the expression of the methionine synthase gene (MET4) is upregulated in FZF1 (a gene encoding a putative zinc finger protein, which is a positive regulator of the transcription of the cytosolic sulfotransferase gene SSU1) overexpression transformant strains, but its exact function is unknown. To gain insight into the function of the MET4 gene, in this study, a MET4 overexpression vector was constructed and transformed into S. uvarum strain A9. The MET4 transformants showed a 20 mM increase in sulfite tolerance compared to the starting strain. Ninety-two differential genes were found in the transcriptome of A9-MET4 compared to the A9 strain, of which 90 were upregulated, and two were downregulated. The results of RT-qPCR analyses confirmed that the expression of the HOMoserine requiring gene (HOM3) in the sulfate assimilation pathway and some fermentation-stress-related genes were upregulated in the transformants. The overexpression of the MET4 gene resulted in a significant increase in sulfite tolerance, the upregulation of fermentation-stress-related gene expression, and significant changes in the transcriptome profile of the S. uvarum strain.

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Transcriptome analysis of diploid and triploid Populus tomentosa

Cited by 4 publications

References 49 publications

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L.

Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in Tetraploid Robinia pseudoacacia L.

Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level

Overexpression of MET4 Leads to the Upregulation of Stress-Related Genes and Enhanced Sulfite Tolerance in Saccharomyces uvarum

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