Comparative Transcriptome Analyses Revealed Conserved and Novel Responses to Cold and Freezing Stress in <i>Brassica napus</i> L

He, Xin; Ni, Xianchao; Xie, Ping; Liu, Wei; Min, Yang Gi; Kang, Yu; Qin, Lunwen; Wei, Hua

doi:10.1534/g3.119.400229

Cited by 36 publications

(34 citation statements)

References 85 publications

(101 reference statements)

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“…To detect the response of BnaTIFY genes to different low temperature stresses, the reads per kilobase of transcripts per million mapped reads (RPKM) values of each gene (Additional file 12 ) in leaves treated with chilling and freezing with or without cold acclimation were determined using the data from GEO (GSE129220) [ 52 ]. As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide identification and functional analysis of the TIFY gene family in the response to multiple stresses in Brassica napus L.

Kang

et al. 2020

BMC Genomics

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Background TIFY is a plant-specific protein family with a diversity of functions in plant development and responses to stress and hormones, which contains JASMONATE ZIM-domain (JAZ), TIFY, PPD and ZML subfamilies. Despite extensive studies of TIFY family in many other species, TIFY has not yet been characterized in Brassica napus. Results In this study, we identified 77, 36 and 39 TIFY family genes in the genome of B. napus, B. rapa and B. oleracea, respectively. Results of the phylogenetic analysis indicated the 170 TIFY proteins from Arabidopsis, B. napus, B. rapa and B. oleracea could be divided into 11 groups: seven JAZ groups, one PPD group, one TIFY group, and two ZIM/ZML groups. The molecular evolutionary analysis showed that TIFY genes were conserved in Brassicaceae species. Gene expression profiling and qRT-PCR revealed that different groups of BnaTIFY members have distinct spatiotemporal expression patterns in normal conditions or following treatment with different abiotic/biotic stresses and hormones. The BnaJAZ subfamily genes were predominantly expressed in roots and up-regulated by NaCl, PEG, freezing, methyl jasmonate (MeJA), salicylic acid (SA) and Sclerotinia sclerotiorum in leaves, suggesting that they have a vital role in hormone signaling to regulate multiple stress tolerance in B. napus. Conclusions The extensive annotation and expression analysis of the BnaTIFY genes contributes to our understanding of the functions of these genes in multiple stress responses and phytohormone crosstalk in B. napus.

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Section: Resultsmentioning

confidence: 99%

Genome-wide identification and functional analysis of the TIFY gene family in the response to multiple stresses in Brassica napus L.

Kang

et al. 2020

BMC Genomics

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“…Nowadays, thousands of genes and many signaling pathways have been identified in numerous plants during cold stress ( Winfield et al, 2010 ), however, a clear and comprehensive relationship between lipid metabolism and cold tolerance has not been established, especially in peanuts. Recent studies suggest that plant hormone signal transduction, photosynthesis, plant-pathogen interaction, and circadian rhythms pathways were essential all play a role in response to cold stress ( Li et al, 2019 ; Ma et al, 2019 ; Xin et al, 2019 ). In this study, these responses also were significantly enriched in two peanut cultivars under cold stress.…”

Section: Discussionmentioning

confidence: 99%

An Advanced Lipid Metabolism System Revealed by Transcriptomic and Lipidomic Analyses Plays a Central Role in Peanut Cold Tolerance

et al. 2020

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Cold stress restricts peanut (Arachis hypogaea L.) growth, development, and yield. However, the specific mechanism of cold tolerance in peanut remains unknown. Here, the comparative physiological, transcriptomic, and lipidomic analyses of cold tolerant variety NH5 and cold sensitive variety FH18 at different time points of cold stress were conducted to fill this gap. Transcriptomic analysis revealed lipid metabolism including membrane lipid and fatty acid metabolism may be a significant contributor in peanut cold tolerance, and 59 cold-tolerant genes involved in lipid metabolism were identified. Lipidomic data corroborated the importance of membrane lipid remodeling and fatty acid unsaturation. It indicated that photosynthetic damage, resulted from the alteration in fluidity and integrity of photosynthetic membranes under cold stress, were mainly caused by markedly decreased monogalactosyldiacylglycerol (MGDG) levels and could be relieved by increased digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG) levels. The upregulation of phosphatidate phosphatase (PAP1) and phosphatidate cytidylyltransferase (CDS1) inhibited the excessive accumulation of PA, thus may prevent the peroxidation of membrane lipids. In addition, fatty acid elongation and fatty acid boxidation were also worth further studied in peanut cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of peanut cold tolerance, in which the advanced lipid metabolism system plays a central role. This study lays the foundation for deeply analyzing the molecular mechanism and realizing the genetic improvement of peanut cold tolerance.

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“…Based on the transcriptional profiling of early-maturing, cultivated B. napus varieties under different low-temperature treatments with or without cold acclimation (GSE129220: https://www.ncbi. nlm.nih.gov/geo/query/acc.cgi?acc=GSE129220) (Table S4) 64 , transcriptome analysis revealed that group III BnaANN were induced slightly by chilling stress, and were up-regulated by freezing stress strongly, regardless of cold acclimation (Fig. 5A).…”

Section: Mw (Kd) Introns Exonsmentioning

confidence: 99%

“…For chilling and freezing treatments with or without cold acclimation, the seedlings of two early-maturing semi-winter rapeseed varieties (HX17 and HX58) were used. They were treated as described previously 64 RnA isolation and sequencing and gene expression analysis. The collected samples were sent to the sequencing cooperations of Sangon Biotech (Shanghai) Co., Ltd. and Novogene Co., Ltd. for RNA isolation, examination, and sequencing 64,85 .…”

Section: Mw (Kd) Introns Exonsmentioning

confidence: 99%

“…They were treated as described previously 64 RnA isolation and sequencing and gene expression analysis. The collected samples were sent to the sequencing cooperations of Sangon Biotech (Shanghai) Co., Ltd. and Novogene Co., Ltd. for RNA isolation, examination, and sequencing 64,85 . qRT-PCR analysis was performed as described previously 85 .…”

Section: Mw (Kd) Introns Exonsmentioning

confidence: 99%

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Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

Liao

Xie

et al. 2020

Sci Rep

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Annexins (Ann) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGcnA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.Annexins (ANN) are a multigene, evolutionarily conserved family of calcium (Ca 2+ )-dependent and phospholipid-binding proteins present in plants, animals, and microorganisms 1,2 . ANN contain the characteristic annexin repeat and they regulate membrane dynamics, mediate Ca 2+ sensing and signaling, link Ca 2+ dynamics to cytoskeletal responses, and mediate immune or stress responses and signaling during plant growth and development 1,3 . A typical ANN contains four annexin repeats at the C-terminal region and a highly variable N-terminal region. Each annexin repeat usually contains a characteristic type II motif for Ca 2+ binding 1,3 . The variable N-terminal region interacts with other proteins and is responsible for the functional diversity of ANN 4 .Recent studies have identified the ANN gene family in Arabidopsis thaliana (8 genes), Brassica rapa (13), Solanum lycopersicum (9), Solanum tuberosum (9), Oryza sativa (10), Triticum aestivum (25), Gossypium raimondii (14), Arachis hypogaea L. (8), Hordeum vulgare (11), Medicago truncatula (10), Populus trichocarpa (12), Vitis vinifera (14), Carica papaya (12), Glycine max (22), Cochliobolus sativus (11), Sorghum bicolor (10), Zea mays (12), Brachypodium distachyon (11), Selaginella mollendorffii (5), and Physcomitrella patens (7) via genome-wide analysis 2,5-11 .Studies have shown that ANN gene family plays a significant role in plant development and plant protection during both abiotic and biotic stresses 1,3,12,13 . In Arabidopsis, two ANN genes (AtANN1 and AtANN4) were regulated by abiotic stress, negatively regulated plant tolerance to drought, salinity, and heat stress, while AtANN8 was open Scientific RepoRtS | (2020) 10:4295 | https://doi.org/10.1038/s41598-020-59953-w www.nature.com/scientificreports www.nature.com/scientificreports/ positive regulated the plant abiotic tolerance [...

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Comparative Transcriptome Analyses Revealed Conserved and Novel Responses to Cold and Freezing Stress in Brassica napus L

Cited by 36 publications

References 85 publications

Genome-wide identification and functional analysis of the TIFY gene family in the response to multiple stresses in Brassica napus L.

Genome-wide identification and functional analysis of the TIFY gene family in the response to multiple stresses in Brassica napus L.

An Advanced Lipid Metabolism System Revealed by Transcriptomic and Lipidomic Analyses Plays a Central Role in Peanut Cold Tolerance

Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response

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