ccNET: Database of co-expression networks with functional modules for diploid and polyploid<i>Gossypium</i>

You, Qi; Xu, Wenying; Zhang, Kang; Zhang, Liwei; Yi, Xin; Yao, Dongxia; Wang, Chunchao; Zhang, Xueyan; Zhao, Xinhua; Provart, Nicholas J.; Li, Fuguang; Su, Zhen

doi:10.1093/nar/gkw910

Cited by 80 publications

(72 citation statements)

References 52 publications

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“…To explore the possibility that more genes from cotton, beyond CYP749A16, are involved in generating TFS herbicide tolerance, we examined expression of select genes by RT-qPCR. We queried the ccNET database with Gh_D10G1401 to find genes that are often co-expressed [ 42 ]. From the list, we selected genes with the highest mutual ranks, plus high ranking P450 genes and genes with no known ortholog in Arabidopsis .…”

Section: Resultsmentioning

confidence: 99%

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The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

et al. 2018

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BackgroundWeed management is critical to global crop production and is complicated by rapidly evolving herbicide resistance in weeds. New sources of herbicide resistance are needed for crop plants so that applied herbicides can be rotated or combined to thwart the evolution of resistant weeds. The diverse family of cytochrome P450 proteins has been suggested to be a source of detoxifying herbicide metabolism in both weed and crop plants, and greater understanding of these genes will offer avenues for crop improvement and novel weed management practices.ResultsHere, we report the identification of CYP749A16 (Gh_D10G1401) which is responsible for the natural tolerance exhibited by most cotton, Gossypium hirsutum L., cultivars to the herbicide trifloxysulfuron sodium (TFS, CGA 362622, commercial formulation Envoke). A 1-bp frameshift insertion in the third exon of CYP749A16 results in the loss of tolerance to TFS. The DNA marker designed from this insertion perfectly co-segregated with the phenotype in 2145 F2 progeny of a cross between the sensitive cultivar Paymaster HS26 and tolerant cultivar Stoneville 474, and in 550 recombinant inbred lines of a multi-parent advanced generation inter-cross population. Marker analysis of 382 additional cotton cultivars identified twelve cultivars containing the 1-bp frameshift insertion. The marker genotypes matched perfectly with phenotypes in 188 plants from the selected twelve cultivars. Virus-induced gene silencing of CYP749A16 generated sensitivity in the tolerant cotton cultivar Stoneville 474.ConclusionsCYP749A16 located on chromosome D10 is required for TFS herbicide tolerance in cotton. This finding should add to the repertoire of tools available to farmers and breeders for the advancement of agricultural productivity.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1414-2) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

“…The ccNet database was queried for co-expressed genes of Gh_D10G1401 [ 42 ]. Twenty genes, including four P450 genes, and eight genes without an obvious ortholog in Arabidopsis were selected for analysis and specific RT-qPCR primers were designed (Additional file 1 : Table S5).…”

Section: Methodsmentioning

confidence: 99%

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

et al. 2018

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“…The expression level of GhPHD genes were extracted from the transcriptome analysis data and heatmap were drawn by TBtools [60]. The ccNET software [62] was used to analyze the co-expression network relation of PHD genes.…”

Section: Identification Of Cis-acting Elements In the Ghphd Promoter mentioning

confidence: 99%

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

Zheng

Qanmber

et al. 2020

Preprint

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Background The sequencing and annotations of cotton genomes provide strong theoretical support to reveal more physiological phenomena and functions. Plant homeodomain (PHD) protein family have been reported to be involved in regulating diverse biological processes in plants. However, their functions have not yet been carried out in cotton. Results In this study, we performed a genome-wide analysis of the PHD genes in cotton, including the chromosomal location, phylogenetic relationship, gene structure, and conserved domains. Using a phylogenetic analysis, we divided the 297 PHD genes into five subgroups. The GhPHDs were unevenly distributed across all 26 chromosomes in upland cotton, and whole genome duplication events analyses showed that purifying selection might contributed greatly to the maintenance of function in the GhPHD family. Expression pattern analysis based on RNA-seq data and qRT-PCR results showed that the most of GhPHD genes have significant tissue-specific spatial and temporal expression patterns, indicating GhPHD have multiple functions in growth and development. We further summarized the cis -acting elements in response to abiotic stresses and plant hormones, and treated cotton seedlings with abiotic stresses and plant hormones, respectively. Then, GhPHD gene expression level were detected by qRT-PCR, which indicated that GhPHD could response to stresses and plant hormones. Co-expression network analysis also indicated that GhPHDs were essential for plant growth and development, and phytohormone mediate GhPHD response to abiotic stress can improve plant tolerance to adverse environment. Conclusion This study provides useful information to facilitate the further study of the function of the GhPHD family.

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“…Co-expression network was constructed as described previously. The adjacent global gene positive and negative co-expression network of the PCG was generated online (http://structuralbiology.cau.edu.cn/gossypium/) [63].…”

Section: Co-expression Networkmentioning

confidence: 99%

The Functional Examination of Conserved and Non-conserved lncRNA in Allotetraploid Gossypium hirsutum

Guan¹,

Wang²,

Han³

et al. 2020

Preprint

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Background The relationship between the lncRNA conservation level and its function is controversial. One of the technique barrier to address this question is how to define the conserved non-coding genes across species.Results We developed an evolutionary model using diploid and allotetraploid cotton species to identify 80% of the non-coding transcripts unique to the allotetraploid cotton in comparison with its diploid ancestors. This led us to define conserved lncRNA and non-conserved lncRNA based on their conservation throughout polyploid evolution. LncRNA expression was preferentially associated with the flanking protein-coding genes, indicating a regulatory role in cis in response to environmental stimuli. However, the conserved and non-conserved lncRNAs showed no difference in their levels of association with the expression of the flanking protein-coding genes. The 111 selected highly expressed conserved and non-conserved lncRNA candidates were subjected to a virus-induced gene silencing operation that was integrated with abiotic stress treatments. From the low-throughput, functional screening pilot test, we obtained candidate lncRNAs related to plant height, tolerance to drought and other abiotic stresses. Conclusions The conservation level of the lncRNAs may impact on their expression patterns and functions as individual case rather than in genome wide.

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ccNET: Database of co-expression networks with functional modules for diploid and polyploidGossypium

Cited by 80 publications

References 52 publications

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)

The Functional Examination of Conserved and Non-conserved lncRNA in Allotetraploid Gossypium hirsutum

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