Genome-wide analysis of the rice J-protein family: identification, genomic organization, and expression profiles under multiple stresses

Abstract

J-proteins which function as molecular chaperone played critical roles in plant growth, development, and response to various environment stresses, but little was reported on this gene family in rice. Here, we identified 115 putative rice J-proteins and classified them into nine major clades (I-IX) according to their phylogenetic relationships. Gene-structure analysis revealed that each member of the same clade has same or similar exon-intron structure, and most rice J-protein genes of clade VII were intronless. Chromosomes mapping suggested that tandem duplication was occurred in evolution. Expression profile showed that the 61 rice J-protein genes were expressed in at least one tissue. The result implied that they could be involved in the process of rice growth and development. The RNA-sequencing data identified 96 differentially expressed genes, 59.38% (57/96), 67.71% (65/96), and 62.50% (60/96) genes were induced by heat stress, drought stress, and salt stress, respectively. The results indicated that J-protein genes could participated in rice response to different stresses. The findings in this study would provide a foundation for further analyzing the function of J-proteins in rice.

Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress

“…Only samples of healthy (mock-inoculated) tissues were analysed here. In the work of Luo et al [ 62 ], the heat stress treatment was applied for 1, 3, 6, 12, and 24 h after the 0 h control. To take full account of the time-of-day variations in gene expression due to photoperiod [ 95 ] and circadian control [ 96 ], only time points 0 h (control) and 24 h (heat stress) were analysed.…”

“…The following are available online at https://www.mdpi.com/article/ 10.3390/plants10081647/s1, Figure S1: Distribution of the number of genes (y-axis) per number of transcripts per gene (x-axis) before (red) and after (blue) filtering low expressed transcripts and genes using the RNA-seq data extracted from Luo et al [62]; Figure S2…”

“…The following are available online at , Figure S1: Distribution of the number of genes (y-axis) per number of transcripts per gene (x-axis) before (red) and after (blue) filtering low expressed transcripts and genes using the RNA-seq data extracted from Luo et al [ 62 ]; Figure S2: Venn diagram showing the overlap of expressed genes from each experiment analysed here; Figure S3: Number of up- and down-regulated genes; Figure S4: GO analysis of DAS genes identified in Experiment 3; Figure S5: Heat-induced changes in transcript expression of two DAS genes; Table S1: Sequencing information for each study analysed here; Table S2: Meta-data table containing experimental design information of 345 RNA-seq datasets analysed here; Table S3: DE and DAS genes IDs and functions, organised by experiment; Table S4: (a) Known heat-response genes, (b) novel heat-response DE and DAS genes, (c) novel DE-only heat shock proteins, transcription factors, epigenetic proteins and splicing-related factors.…”

“…Datasets for this research are included in [ 14 , 19 , 20 , 22 , 62 ]. The script used to carry out the data mining analysis is available at .…”

Drought Stress Induces Morpho-physiological and Proteome Changes ofPandanus amaryllifolius

“…For instance, HSP70 in peanut was increased in abundance in response to drought [32]. DnaJ homolog proteins are essential components in the chaperone machine and could be induced by cold [33], heat [34], and drought stresses [35,36]. Other studies showed that several HSPs, co-chaperone DnaJ, and Grp chaperonin 60b were differentially altered under drought conditions [37,38].…”