Comparative transcriptome analysis of the floral transition in Rosa chinensis ‘Old Blush’ and R. odorata var. gigantea

Guo, Xijie; Yu, Chao; Luo, Le; Wan, Huihua; Li, Yushu; Wang, Jia; Cheng, Tangren; Zhang, Qixiang

doi:10.1038/s41598-017-05850-8

Cited by 17 publications

(26 citation statements)

References 61 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this work, many DEGs and DEPs were identified between the two types of pineapple, namely, CP and SC, which are categorized as Queen and Cayenne, respectively, before the ethephon induction treatment, which suggested that there are basic differences between CP and SC. Similar results occurred in the reports of the seasonal and continuous flowering roses in response to floral transition [34] as well as for low-and high-cadmium-accumulating genotypes of pakchoi (Brassica chinensis L.) in response to cadmium stress [35]. In particular, the results revealed that the expression levels of the ETR and ERF genes were lower in CP than in SC before the ethephon induction treatment, whereas those of the ACS and ACO genes were higher.…”

Section: Variation In the Basic Ability Of Ethylene Signal Transductisupporting

confidence: 75%

“…Increases in soluble sugar concentrations in the apical meristem represent one of the first physiological changes in plants and sugar and starch metabolism play vital roles in the regulation of the floral transition [34,40]. In the present work, the expression of the SPS, FBP and BAM genes and of some sugar metabolic proteins (GluPAT and BGLU) were upregulated and were found to be higher in CP than in SC after ethephon application.…”

Section: Expression Of Floral Induction-related Degs and Deps Respondmentioning

confidence: 58%

“…However, more carbohydrate metabolism, plant hormone signal transduction and metabolism-associated GO terms and KEGG metabolic pathways with more DEGs were enriched in the CP-T and CP-CK comparison group than in the SC-T and SC-CK comparison group. In addition, a few photoperiodism-related GO terms, including photosynthesis, light reaction and photosynthesis, and light harvesting as well as KEGG pathways, namely, photosynthesis and circadian rhythm-plant [34], were annotated in the CP-T and CP-CK comparison group. Combined with the photoperiod pathway-associated DEGs, COR27 and GI [42,53], identified in CP (not showed), these results suggested that ethephon induction probably triggered the photoperiod pathway for floral initiation in the CP pineapple plants, whereas the corresponding photoperiod pathway was not triggered in the SC plants.…”

Section: More Tfs Responded To Ethephon Stimulation In Sc After Ethepmentioning

confidence: 99%

See 2 more Smart Citations

Comparative Analyses of the Transcriptome and Proteome of Comte de Paris and Smooth Cayenne to Improve the Understanding of Ethephon-Induced Floral Transition in Pineapple

Liu¹,

Liu²,

Shao³

et al. 2018

Cell Physiol Biochem

View full text Add to dashboard Cite

Background/Aims: Ethylene is usually used to induce floral transition in pineapple. However, its successful induction in plants categorized as Cayenne is difficult or completely ineffective, and information concerned is limited. The present study was undertaken to investigate the molecular mechanisms underlying this obstacle. Methods: Transcriptome and proteome comparative analyses were performed to explore the important regulation and pathway variations after ethephon induction in the induction-easy ‘Comte de Paris’ (CP) and induction-hard ‘Smooth Cayenne’ (SC) cultivars via RNA-seq (RNA-sequencing) and iTRAQ (isobaric tags for relative and absolute quantification). Results: CP and SC exhibited basic differences at the transcriptomic and proteomic levels before ethephon treatment, including the expression of genes and proteins related to ethylene signal transduction. After ethephon induction, the expression of genes and proteins involved in plant ethylene signal transduction and carbohydrate metabolism responded more strongly in CP than in SC. The expression of the floral meristem identity (FMI) genes AG, TFL and FT exhibited greater changes in CP, and more transcription factors responded in SC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that many differentially expressed genes (DEGs) in CP were annotated to terms and pathways involved in photoperiodism and shared components involved in carbohydrate metabolism and plant hormone signal transduction. Conclusion: These findings contribute to the understanding of the molecular mechanism underlying the variation between CP and SC in response to ethephon-mediated floral induction.

show abstract

Section: Variation In the Basic Ability Of Ethylene Signal Transductisupporting

confidence: 75%

Section: Expression Of Floral Induction-related Degs and Deps Respondmentioning

confidence: 58%

Section: More Tfs Responded To Ethephon Stimulation In Sc After Ethepmentioning

confidence: 99%

See 1 more Smart Citation

Comparative Analyses of the Transcriptome and Proteome of Comte de Paris and Smooth Cayenne to Improve the Understanding of Ethephon-Induced Floral Transition in Pineapple

Liu¹,

Liu²,

Shao³

et al. 2018

Cell Physiol Biochem

View full text Add to dashboard Cite

show abstract

“…Clustering pattern analysis of gene expression is commonly used in transcriptome research [34][35][36]. However, we found that some DEGs identified by clustering pattern in this study were differentially expressed in both cultivars of P. rockii, which limited the identification of specific factors.…”

Section: Wgcna Of Carpel Quantitative Variation In P Rockiimentioning

confidence: 59%

“…RNA-seq technology is an important method to obtain effective functional genes in crops, especially for crops without reference genomic information. At present, RNA-seq has been widely used to study floral organ development in woody plants [32][33][34][35][36]. With the development of highthroughput sequencing technology, numerous studies have been carried out by SMLRS or in combination with NGS technology.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

et al. 2019

View full text Add to dashboard Cite

Background Quantitative variation of floral organs in plants is caused by an extremely complex process of transcriptional regulation. Despite progress in model plants, the molecular mechanisms of quantitative variation remain unknown in woody flower plants. The Paeonia rockii originated in China is a precious woody plant with ornamental, medicinal and oil properties. There is a wide variation in the number of carpel in P. rockii , but the molecular mechanism of the variation has rarely been studied. Then a comparative transcriptome was performed among two cultivars of P. rockii with different development patterns of carpel in this study. Results Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in P. rockii . Then clustering pattern and weighted gene coexpression network analysis (WGCNA) indicated that 15 candidate genes were likely involved in the carpel quantitative variation, including floral organ development, transcriptional regulatory and enzyme-like factors. Moreover, transcription factors (TFs) from the MYB, WD, RING1 and LRR gene families suggested the important roles in the management of the upstream genes. Among them, PsMYB114-like , PsMYB12 and PsMYB61-like from the MYB gene family were probably the main characters that regulated the carpel quantitative variation. Further, a hypothetical model for the regulation pattern of carpel quantitative variation was proposed in which the candidate genes function synergistically the quantitative variation process. Conclusions We present the high-quality sequencing products in P. rockii . Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. The DEGs are candidate for functional analyses of genes regulating the carpel quantitative variation in tree peonies, which provide a precious resource that reveals the molecular mechanism of carpel quantitative variation in other woody flower crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-6036-z) contains supplementary material, which is available to authorized users.

show abstract

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

Zhao

Yin

et al. 2020

FEBS Open Bio

View full text Add to dashboard Cite

Goji berries have been used as food and medicine for millennia. Due to their high morphological similarity, fruits of two distinct species belonging to the family Solanaceae, Lycium barbarum (LB) and Lycium chinense (Chinese boxthorn), are usually marketed together as goji berries, but nearly 90% of all commercially available goji berries belong to the former species. A third closely related species, a wild perennial thorny shrub native to north‐western China, Lycium ruthenicum (LR; known as Russian box thorn, and its fruit as black wolfberry), has become a popular choice for combating soil desertification and for alleviating soil salinity/alkalinity due to its high resistance to the harsh environment of saline deserts. Despite the phylogenetic closeness of LB and LR, their fruits are very different. To identify the genes involved in these distinct phenotypes, here we studied expression patterns of 22 transcriptional regulators that may be crucial drivers of these differences during five developmental stages. BAM1 may contribute to higher sugar content in LB. High expression of BFRUCT in ripe LR is likely to be an evolutionary adaptation to fruit ripening in an arid environment. Two arogenate dehydratase paralogues, CHS and LDOX, are probably crucial elements of the mechanism by which LR accumulates much higher levels of anthocyanin. DXS2 (carotenoid accumulation in LB) and CCD4 (carotenoid degradation in ripe LR fruit) may be crucial drivers behind the much higher content of carotenoids in LB. EIL3 and ERF5 are two transcription factors that may contribute to the higher abiotic stress resilience of LR. GATA22‐like appears to have more important roles in growth than ripening in LB fruit and vice versa in LR. HAT5‐like exhibited opposite temporal patterns in two fruits: high in the 1st stage in LB and high in the 5th stage in LR. PED1 was expressed at a much lower level in LR. Finally, we hypothesise that the poorly functionally characterised SCL32 gene may play a part in the increased resistance to environmental stress of LR. We suggest that BAM1, BFRUCT, EIL3, ERF5, ADT paralogues (for functional redundancy), PED1, GATA22‐like, HAT5‐like and SCL32 warrant further functional studies.

show abstract

Comparative transcriptome analysis of the floral transition in Rosa chinensis ‘Old Blush’ and R. odorata var. gigantea

Cited by 17 publications

References 61 publications

Comparative Analyses of the Transcriptome and Proteome of Comte de Paris and Smooth Cayenne to Improve the Understanding of Ethephon-Induced Floral Transition in Pineapple

Comparative Analyses of the Transcriptome and Proteome of Comte de Paris and Smooth Cayenne to Improve the Understanding of Ethephon-Induced Floral Transition in Pineapple

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

Contact Info

Product

Resources

About