Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry

Shahan, Rachel; Zawora, Christopher; Wight, Haley; Sittmann, John; Wang, Wanpeng; Mount, Stephen M.; Liu, Zhongchi

doi:10.1104/pp.18.00086

Cited by 63 publications

(62 citation statements)

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“…F. vesca genome V4.0a2 has about 34 FveARFs and 25 FveIAAs (Edger et al, 2018; Li et al, 2019). To identify candidate FveIAAs, we mined the consensus co-expression network generated previously (Shahan et al, 2018) (http://159.203.72.198:3838/fvesca/). FveARF8 resides in module 80 of the Consensus_90 Fruit Network; this module 80 correlates positively in expression with early stage receptacle fruit tissues.…”

Section: Resultsmentioning

confidence: 99%

“…Previously, a consensus-clustering approach was applied to the standard WGCNA (Weighted Gene Co-expression Network Analysis) to generate robust and reproducible modules (Shahan et al, 2018). Since ARF and IAA genes are from large gene families, the consensus co-expression network led us to a co-expression module consisting of FveIAA4, FveARF6 and FveARF8 (Figure 6A).…”

Section: Discussionmentioning

confidence: 99%

“…The expression pattern of each F. vesca gene in wild type (YW5AF7) was visualized via strawberry eFP browser (Hawkins et al, 2017) (http://mb3.towson.edu/efp/cgi-bin/efpWeb.cgi). The consensus co-expression network analysis of YW5AF7 floral and fruit tissues(Shahan et al, 2018) was mined using the network website (http://159.203.72.198:3838/fvesca/). The co-expression cluster/module was visualized using Cytoscape (cytoscape.org).…”

Section: Methodsmentioning

confidence: 99%

“…The unique strawberry fruit structure as well as prior research provide a strong foundation for further investigations into signal communication between achenes and the receptacle and auxin/GA crosstalk during fruit development. This is further aided by the rich genomic resources including genome sequencing of wild strawberry Fragaria vesca and garden strawberry Fragaria x ananassa (Shulaev et al, 2011; Edger et al, 2018; Edger et al, 2019) as well as extensive transcriptome data and network analyses during flower and fruit development (Kang et al, 2013; Hollender et al, 2014; Sanchez-Sevilla et al, 2017; Shahan et al, 2018). As garden strawberry is an allo-octoploid, wild strawberry F. vesca, a diploid species, is used in this study.…”

Section: Introductionmentioning

confidence: 99%

“…However, auxin and GA perception and signaling genes, TIR/IAAs and GID1c/RGA1, are highly expressed in the receptacle, indicating receptacle as the site of auxin and GA perception and response (Kang et al, 2013). Using the RNA-seq data described above, consensus co-expression network was established (Shahan et al, 2018), which identifies robust co-expression modules in receptacle fruit development. In addition, CRISPR/Cas9 genome editing has been demonstrated in wild and garden strawberries (Zhou et al, 2018; Feng et al, 2019; Martin-Pizarro et al, 2019), providing tools for dissecting gene function.…”

Section: Introductionmentioning

confidence: 99%

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Mechanism of auxin and GA crosstalk in diploid strawberry fruit initiation

Zhou

Sittmann

Guo

et al. 2020

Preprint

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Strawberry, a high value fruit crop, has recently become amenable for genetic studies due to genomic resources and CRISPR/CAS9 tools. Unlike ovary-derived botanical fruits, strawberry is an accessory fruit derived from receptacle, the stem tip subtending floral organs. Although both botanical and accessory fruits initiate development in response to auxin and GA released from seeds, the downstream auxin and GA signaling mechanisms underlying accessory fruit development remain unknown. Using wild strawberry, we performed in depth molecular characterizations of accessory fruit development. We show that auxin signaling proteins FveARF8/FveARF6 are bound and hence inhibited by FveIAA4 and FveRGA1, repressors in auxin and GA signaling pathways. This inhibition is relieved post-fertilization or by the application of GA or auxin. Mutants of FveRGA1 developed parthenocarpic fruit suggesting a conserved function of DELLA proteins in fruit set. Further, FveARF8 was found to repress the expression of a GA receptor gene GID1c to control fruit’s sensitivity to GA, revealing a novel crosstalk mechanism. We demonstrate that consensus co-expression network provides a powerful tool for non-model species in the selection of interacting genes for functional studies. These findings will facilitate the improvement of strawberry fruit productivity and quality by guiding future production of parthenocarpic fruit.One sentence summaryGenome editing and network analysis are applied to investigating the mechanism of accessory fruit initiation in the wild strawberry, revealing conserved as well as novel crosstalk mechanisms.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Zhongchi Liu (zliu@umd.edu)

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mechanism of auxin and GA crosstalk in diploid strawberry fruit initiation

Zhou

Sittmann

Guo

et al. 2020

Preprint

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Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

García‐Blay,

Verhagen,

Martin

et al. 2023

BioEssays

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Co‐expression of two or more genes at the single‐cell level is usually associated with functional co‐regulation. While mRNA co‐expression—measured as the correlation in mRNA levels—can be influenced by both transcriptional and post‐transcriptional events, transcriptional regulation is typically considered dominant. We review and connect the literature describing transcriptional and post‐transcriptional regulation of co‐expression. To enhance our understanding, we integrate four datasets spanning single‐cell gene expression data, single‐cell promoter activity data and individual transcript half‐lives. Confirming expectations, we find that positive co‐expression necessitates promoter coordination and similar mRNA half‐lives. Surprisingly, negative co‐expression is favored by differences in mRNA half‐lives, contrary to initial predictions from stochastic simulations. Notably, this association manifests specifically within clusters of genes. We further observe a striking compensation between promoter coordination and mRNA half‐lives, which additional stochastic simulations suggest might give rise to the observed co‐expression patterns. These findings raise intriguing questions about the functional advantages conferred by this compensation between distal kinetic steps.

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Gene Co-expression Network Analysis

Montenegro

2022

Methods in Molecular Biology

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Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry

Cited by 63 publications

References 70 publications

Mechanism of auxin and GA crosstalk in diploid strawberry fruit initiation

Mechanism of auxin and GA crosstalk in diploid strawberry fruit initiation

Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression

Gene Co-expression Network Analysis

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