Cold stress regulation of gene expression in plants

Chinnusamy, Viswanathan; Zhu, Jianhua; Zhu, Jian‐Kang

doi:10.1016/j.tplants.2007.07.002

Cited by 1,709 publications

(1,398 citation statements)

References 74 publications

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“…Seedlings transferred to cold exhibited a strong and transient induction of cold-inducible CBF transcription factor genes ( Figure 1d) (Thomashow, 1999;Chinnusamy et al, 2007). Our conditions are thus comparable to stress situations examined previously.…”

Section: Resultssupporting

confidence: 81%

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

et al. 2009

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SUMMARYThe responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.

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Section: Resultssupporting

confidence: 81%

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

et al. 2009

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“…In addition, dehydrins, which play a role in the response to cold/drought 44 , had only two members in G. montanum, compared with 38 in P. abies, 28 in P. taeda and 3-15 in angiosperms (Supplementary Table 19). Further analysis of the G. montanum genome also revealed relatively few gene family members of the AP2 domain containing protein families, which are involved in the cold stress response 45,46 , and glutathione peroxidase and glutathione S-transferase families, involved in the oxidant stress response 47,48 . Taken together, these data appear consistent with the hypothesis that the ecological shift to a warm, wet forest habitat is associated with a relaxation of selection pressure on genes associated with water stress and low temperature.…”

Section: Water Stressmentioning

confidence: 99%

A genome for gnetophytes and early evolution of seed plants

et al. 2018

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Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms. NATuRe PLANTS ArticlesNATurE PLANTs phylogenetic position of gnetophytes, with topologies differing depending on the type of sequence data (for example, plastid versus nuclear genes, nucleotide versus amino acid data) and analytical approach used (for example, maximum parsimony, maximum likelihood, Bayesian, multispecies coalescent based methods) [6][7][8] . Consequently, several possible hypotheses have been put forward that place gnetophytes as sister to (1) Pinaceae ('Gnepine' hypothesis); (2) cupressophytes ('Gnecup' hypothesis); (3) all conifers ('Gnetifer' hypothesis); (4) all other gymnosperms; or (5) all seed plants 9 . Currently, the emerging consensus, based on both older and more recent studies, and recently released data from the 1KP initiative (see https://sites.google.com/a/ualberta.ca/onekp/, and Wickett et al. 8 ), indicates that gnetophytes are sister to, or within, the conifers.So far, the availability of whole genome sequences for gymnosperms has been limited to conifers (specifically to Pinaceae) [10][11][12][13] and G. biloba 14 , with no whole genome assemblies available for the two remaining major seed plant lineages-cycads and gnetophytes. This deficiency, together with the conflicting phylogenetic evidence for relationships among these groups, is impeding our understanding of genome evolution across all seed plants. Here, we present a high-quality draft genome of Gnetum ...

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“…In land plants and green algae, the important role of transcription factors during stress responses and development has been demonstrated. For example, CBF1, 2 and 3 direct cold-inducible gene expression in Arabidopsis thaliana (Chinnusamy et al 2007), while Myb transcription factor LCR1 regulates the CO 2 responsive gene Cah1 under CO 2 limiting stress in Chlamydomonas reinhardtii (Yoshioka et al 2004). Moreover, in Volvox carteri, RegA plays a central role as a master regulatory gene in germ-soma differentiation by suppression of reproductive activities in somatic cells (Babinger et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

et al. 2009

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Running titleFollowing molecular cloning and characterization of transcription factors DP-E2F-like 1 (PyDEL1), transcription elongation factor 1 (PyElf1) and multiprotein bridging factor 1 (PyMBF1), we then demonstrated that ZsGFP and AmCFP can be used to visualize nuclear localization of PyElf1 and PyMBF1. This is the first report to perform visualization of subcellular localization of transcription factors as genome-encoded proteins in red algae.3

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Cold stress regulation of gene expression in plants

Cited by 1,709 publications

References 74 publications

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

A genome for gnetophytes and early evolution of seed plants

Visualization of Nuclear Localization of Transcription Factors with Cyan and Green Fluorescent Proteins in the Red Alga Porphyra yezoensis

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