Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Next-generation sequencing analyses of the differently expressed genes of wild type and atcep1 mutant Arabidopsis thaliana

ABSTRACT: Purpose: The goal of this study is to compare the differently expressed genes in the wild type and the KDEL-tailed cysteine protease AtCEP1 knockout (atcep1) Arabidopsis using RNA-sequencing (RNA-seq). Methods: Arabidopsis buds mRNA profiles of anther development stages 5-6, 7-9, and 10-11 of the wild type (WT) and atcep1 mutant were generated by deep sequencing via Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with the following steps: Remove reads with adaptor sequences; Remove reads in which the percentage of unknown bases (N) is greater than 10%; Remove low quality reads, in which the percentage of the low quality base (base with quality value â¤ 5) is greater than 50%. The clean reads were mapped to the Arabidopsis reference genome and reference genes using SOAP aligner/SOAP2. No more than 2 mismatches were allowed in the alignment. The gene expression level was calculated using RPKM (Reads Per Kb per Million reads). Differential expression analysis between the wild type and the atcep1 mutant was performed using the DEGseq R package (1.12.0) based on normalized read counts. A corrected P value of < 0.005 and |log2Ratio| > 1 were set as the threshold for significantly differential expression. Results: We identified 872 genes showing significant differential expression, and in the atcep1 mutant, the upregulated genes significantly outnumbered the downregulated genes at the three time points. The GO analysis of the differently expressed genes showed that the expression of genes participating in anther tapetal secretory structure formation, pollen wall development, and tapetal cell wall generation, clearly changed. Arabidopsis buds mRNA profiles of development stages 5-6, 7-9, and 10-11 of the wild type (WT) and atcep1 muant were generated by deep sequencing via Illumina HiSeqTM 2000.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: dan Zhang

PROVIDER: E-GEOD-50956 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The cysteine protease CEP1, a key executor involved in tapetal programmed cell death, regulates pollen development in Arabidopsis.

Zhang Dandan D Liu Di D Lv Xiaomeng X Wang Ying Y Xun Zhili Z Liu Zhixiong Z Li Fenglan F Lu Hai H

The Plant cell 20140717 7

Tapetal programmed cell death (PCD) is a prerequisite for pollen grain development in angiosperms, and cysteine proteases are the most ubiquitous hydrolases involved in plant PCD. We identified a papain-like cysteine protease, CEP1, which is involved in tapetal PCD and pollen development in Arabidopsis thaliana. CEP1 is expressed specifically in the tapetum from stages 5 to 11 of anther development. The CEP1 protein first appears as a proenzyme in precursor protease vesicles and is then transpor ...[more]

PMID: 25035401

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Project description:Purpose: RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. Methods: mRNA profiles of Aureococcus anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed by aligning to reference genome and transcript using SOAPaligner/SOAP2 (version 2.21). Results: Deconvolution and filtering of raw reads yielded a mean of 6,938,798 reads (range: 6,539,842 to 7,242,083 reads) per individual RNA-seq library (Table 1). Subsequent alignment of the clean reads to the A. anophagefferens reference genome yielded a mean of 5,852,408 reads (84.3%) for each sample that mapped to at least one location in the A. anophagefferens genome. However, of these mapped reads, only 47.4 to 50.9% of the total reads were mapped to the reference transcript for each sample (Table 2). In A. anophagefferens grown on three different N sources, 9148 to 9526 genes were detected for each sample. A comparison of gene expression among the three N sources was performed. 322 differentially expressed genes were detected between nitrate-grown and urea-grown cells, 237 between nitrate-grown and mixture N-grown cells and 29 between urea-grown and mixture N-grown cells. Fewer differentially expressed genes between urea-grown and mixture N-grown cells were identified, which further suggested the preferred utilization of cells for urea in media with mixture N. For nitrogen-limited and recovery experiments, 707 genes were up-regulated significantly, and 766 were down-regulated significantly in N-depleted cells relative to N-replete cells. N-depleted cells exhibited a broad transcriptional response to nitrogen re-addition, with 681 genes up-regulated and 874 genes down-regulated in urea recovery cells, and 312 genes up-regulated and 688 genes down-regulated in nitrate recovery cells. Conclusions: We noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid, nucleotide and aminosugar transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source. Seven mRNA samples for Aureococcus anophagefferens were sequencd using Illumina HiSeqTM 2000, including three samples that was grown on urea, nitrate, and a mixture of urea and nitrate, and four samples that was under N-replete, limited and recovery conditions

Dataset Information

Next-generation sequencing analyses of the differently expressed genes of wild type and atcep1 mutant Arabidopsis thaliana

Publications

The cysteine protease CEP1, a key executor involved in tapetal programmed cell death, regulates pollen development in Arabidopsis.

Similar Datasets

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