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Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

ABSTRACT: To reveal the molecular mechanism of leaf color changes in Acer pictum subsp. mono, this study was conducted on bud-transformed branches, analyzing the transcriptome and small RNAs of Acer pictum subsp. mono leaves and performing miRNA-mRNA association analysis on differentially expressed mRNAs and miRNAs.

ORGANISM(S): Acer pictum subsp. mono

PROVIDER: GSE212815 | GEO | 2022/09/09

REPOSITORIES: GEO

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Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

Project description:To reveal the molecular mechanism of leaf color changes in Acer pictum subsp. mono, this study was conducted on bud-transformed branches, analyzing the transcriptome and small RNAs of Acer pictum subsp. mono leaves and performing miRNA-mRNA association analysis on differentially expressed mRNAs and miRNAs.

2022-09-06 | GSE212656 | GEO

Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

Project description:Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

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Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

Project description:Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of Acer pictum subsp. mono.

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Regulatory mechanisms and metabolic changes of miRNA during leaf color change in the bud mutation branches of <i>Acer pictum subsp</i>. <i>mono</i>.

Project description:Acer pictum subsp. mono is a colorful tree species with considerable ornamental and economic value. However, little is known about the metabolism and regulatory mechanism of leaf color change in A. p. subsp. mono. To reveal the molecular mechanism of leaf color change in A. p. subsp. mono, the present study examined the bud mutation branches and compared the metabolites of the red leaves (AR) of the bud mutation branches of A. p. subsp. mono with those of the green leaves (AG) of the wild-type branches. It was found that the chlorophyll and carotenoids content of the red leaves decreased significantly, while anthocyanins, and various antioxidant enzymes increased significantly compared with the green leaves. The glycosides cyanidin, pelargonidin, malvidin, petunidin, delphinidin, and peonidin were detected in AR by liquid chromatography-mass spectrometry. The cyanidin glycosides increased, and cyanidin 3-O-glycoside was significantly upregulated. We analyzed the transcriptome and small RNA of A. p. subsp. mono leaves and detected 4061 differentially expressed mRNAs and 116 differentially expressed miRNAs. Through miRNA-mRNA association analysis, five differentially expressed modules were found; one miRNA targeted three genes, and four miRNAs targeted a single gene. Among them, miR160b, miR6300, and miR396g were found to be the key miRNAs regulating stable anthocyanin accumulation in A. p. subsp. mono leaves. By revealing the physiological response of leaf color change and the molecular regulatory mechanism of the miRNA, this study provides new insight into the molecular regulatory mechanism of leaf color change, thereby offering a foundation for future studies.

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Transcriptome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition [RNA-seq]

Project description:To investigate the cooperation of light drought with flower branches building and flower bud formation in Citrus, we set two groups including 75 days light drought (LD) and CK to uncover which target genes relatived to flower bud and branches building have been influenced by LD. We then performed gene expression profiling analysis using data obtained from RNA-seq of two different treatment.

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Comparison of pear ‘La France’ and its bud mutant ‘Giant Laf’ (2010 expt, receptacle at 1 week before full bloom stage)

Project description:Bud mutation (bud sport) is mutation occurred in one branch in a tree and the mutant branch shows different phenotype from normal branches. Because bud mutation occurs in a part of plant body, genomic backgrounds of mutant branch and normal branches are the same, except some mutations. Therefore bud mutants are ideal material to identify key genes for important traits of crops. We studied ‘Giant Laf’, a bud mutant setting large fruit, which generated spontaneously in European pear ‘La France’ tree. In ‘Giant Laf’, increase of cell size and DNA reduplication occurred specifically in fruit flesh. The DNA reduplication in ‘Giant Laf’ was observed at 1 week before full bloom stage. This suggested that DNA reduplication observed in ‘Giant Laf’ fruit is not endoreduplication, but endomitosis or nuclear fusion. To identify genes expressed differentially between in ‘Giant Laf’ and in ‘La France’, microarray analysis was performed with RNA from receptacle (fruit flesh) at 1 week before full bloom stage. To isolate the receptacle, laser microdissection was applied. Genes encoding proteins localized in nucleus and cytoskeleton were up-regulated in ‘Giant Laf’. Among these genes, we found several genes which shared homology with previously described DNA reduplication related genes. These are candidates of responsible gene of ‘Giant Laf’ mutation.

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Project description:Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and promising probiotic candidate, showed antagonistic and protective effects against Salmonella and Listeria in vitro. However, the underlying mechanisms fostering these health-related effects remain unknown. Therefor the transcriptome response of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) in co-culture compared to the response in their respective mono-cultures. RNA was extracted from culture samples taken after 4 (N-15) or 5 h (RBL67) and RNAseq was performed on an Illumina HiSeq 2000 sequencer. Three biological replciates were performed resulting in 12 data sets: 3 RBL67 mono culture, 3 N15 mono-culture, 3 RBL67 co-culture, 3 N15 co-culture. Our study provided first insights into probiotic-pathogen interaction on transcriptional level and suggests a mechanism for how probiotic organisms can protect the host from infections.

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Transcriptome response of Salmonella enterica subsp. enterica serovar Typhimurium N-15 and Bifidobacterium thermophilum RBL67 in co-culture

2015-03-31 | E-GEOD-65716 | biostudies-arrayexpress

Comparison of pear M-bM-^@M-^XLa FranceM-bM-^@M-^Y and its bud mutant M-bM-^@M-^XGiant LafM-bM-^@M-^Y (2010 expt, receptacle at 1 week before full bloom stage)

Project description:Bud mutation (bud sport) is mutation occurred in one branch in a tree and the mutant branch shows different phenotype from normal branches. Because bud mutation occurs in a part of plant body, genomic backgrounds of mutant branch and normal branches are the same, except some mutations. Therefore bud mutants are ideal material to identify key genes for important traits of crops. We studied M-bM-^@M-^XGiant LafM-bM-^@M-^Y, a bud mutant setting large fruit, which generated spontaneously in European pear M-bM-^@M-^XLa FranceM-bM-^@M-^Y tree. In M-bM-^@M-^XGiant LafM-bM-^@M-^Y, increase of cell size and DNA reduplication occurred specifically in fruit flesh. The DNA reduplication in M-bM-^@M-^XGiant LafM-bM-^@M-^Y was observed at 1 week before full bloom stage. This suggested that DNA reduplication observed in M-bM-^@M-^XGiant LafM-bM-^@M-^Y fruit is not endoreduplication, but endomitosis or nuclear fusion. To identify genes expressed differentially between in M-bM-^@M-^XGiant LafM-bM-^@M-^Y and in M-bM-^@M-^XLa FranceM-bM-^@M-^Y, microarray analysis was performed with RNA from receptacle (fruit flesh) at 1 week before full bloom stage. To isolate the receptacle, laser microdissection was applied. Genes encoding proteins localized in nucleus and cytoskeleton were up-regulated in M-bM-^@M-^XGiant LafM-bM-^@M-^Y. Among these genes, we found several genes which shared homology with previously described DNA reduplication related genes. These are candidates of responsible gene of M-bM-^@M-^XGiant LafM-bM-^@M-^Y mutation. The gene expression profiles between European pear (Pyrus communis) M-bM-^@M-^XLa FranceM-bM-^@M-^Y and its bud mutant M-bM-^@M-^XGiant LafM-bM-^@M-^Y were compared. RNA was extracted from receptacle which was isolated from flower bud at 1 week before full bloom stage by using laser microdissection. Three biological replications were analyzed.

2012-12-31 | E-GEOD-38550 | biostudies-arrayexpress

LFQ of Campylobacter fetus subsp. fetus strains

Project description:Comparsion of proteomes of Campylobacter fetus subsp. fetus to compare protein level via iBAQ analysis, expression (by LFQ) and coverage between Campylobacter fetus subsp. fetus strain82-40 vs Campylobacter fetus subsp. fetus strain ATCC 27374

2020-05-25 | PXD014538 | Pride

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