iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

Yao-zhao, XU; Zeng, Xiucun; Wu, Jian; Zhang, Fenqin; Li, Caixia; Jiang, Jinjin; Wang, Youping; Sun, Weizheng

doi:10.3390/ijms19113346

Cited by 39 publications

(34 citation statements)

References 83 publications

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“…Among the biological process categorized by GO classi cation, metabolic process and cellular process emerged as the predominant positions, indicating the occurrence of important cellular and metabolic activities in P. ternate. For the molecular function category, catalytic activity and binding were the most highly represented GO terms, which are the similar results to reported studies [37,38]. The most abundant classes, cell and cell part, could not be matched to the previous reports, suggesting there is a limited information of genes functions of P.…”

Section: Discussionsupporting

confidence: 80%

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Lai

Wan

et al. 2020

Preprint

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Background Pinellia ternate (Thunb.) Breit. ( P. ternate ), a weed species distributed in Eastern Asia, has been widely used as a Chinese herbal medicine. Currently, four genotypes of P. ternate have been identified according to their different leaf shapes, including Shaoye, Taoye, Zhuye and Liuye Type. In addition, the total alkaloids and organic acids content in tuber, tuber yields and other physiology and agronomic characteristics were significant difference. However, little is known about the evolution and genetic diversity of four genotypes of P. ternate . Moreover, the genomics of P. ternate remains uncharacterized. The recent development of RNA-Seq, a next generation sequencing technology, provides an opportunity to expand the identification of P. ternate genes through in-depth transcript profiling. Methods In this study, we presented a comprehensive landscape of the transcriptome profiles of four genotypes of P. ternate using Illumina paired-end sequencing technology. Results Totally, 70,491,871, 72,819,035, 73,159,913 and 71,612,115 reads were achieved in four genotypes of P. ternate , respectively. A total number of 126,391 assembled unigenes were identified. After aligning the sequences to the public protein databases, 82,998 unigenes were annotated. Among these, 15,534 were assigned to Gene Ontology categories, 41,216 to Clusters of Orthologous Groups, and 46,053 to Kyoto Encyclopedia of Genes and Genomes pathways. In addition, 23,678 simple sequence repeats (SSRs) and 65,527 Single Nucleotide Polymorphism (SNP) variations were detected. Conclusion This study provides abundant genomic data and comprehensive transcriptome for P. ternate . We envision that these transcriptome datasets will serve as an important public information platform to accelerate further studies of the P. ternate and the identification of genes that potentially involving in the biosynthesis of total alkaloids, acid and other active ingredients among different genotypes P. ternate .

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Section: Discussionsupporting

confidence: 80%

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Lai

Wan

et al. 2020

Preprint

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“…These results reflect that there may be different metabolic patterns in the peroxisome pathway of Longyou-7 and Lenox. The tolerance of Longyou-7 to chilling injury is related to the enhancement of antioxidant enzymes under cold stress [ 48 ]. In the present study, 31 and 26 genes of the peroxisome pathway were enriched in Longyou-7 and Lenox, respectively.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Coulter

Liu³

et al. 2019

IJMS

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Low ambient air temperature limits the growth and selection of crops in cold regions, and cold tolerance is a survival strategy for overwintering plants in cold winters. Studies of differences in transcriptional levels of winter rapeseed (Brassica rapa L.) under cold stress can improve our understanding of transcript-mediated cold stress responses. In this study, two winter rapeseed varieties, Longyou-7 (cold-tolerant) and Lenox (cold-sensitive), were used to reveal morphological, physiological, and transcriptome levels after 24 h of cold stress, and 24 h at room temperature, to identify the mechanism of tolerance to cold stress. Compared to Lenox, Longyou-7 has a shorter growth period and greater belowground mass, and exhibits stronger physiological activity after cold stress. Subsequently, more complete genomic annotation was obtained by sequencing. A total of 10,251 and 10,972 differentially expressed genes (DEG) were identified in Longyou-7 and Lenox, respectively. Six terms closely related to cold stress were found by the Gene Ontology (GO) function annotation. Some of these terms had greater upregulated expression in Longyou-7, and the expression of these genes was verified by qRT-PCR. Most of these DEGs are involved in phenylpropanoid biosynthesis, plant hormone signal transduction, ribosome biogenesis, MAPK signaling pathway, basal transcription factors, and photosynthesis. Analysis of the genes involved in the peroxisome pathway revealed that Longyou-7 and Lenox may have different metabolic patterns. Some transcription factors may play an important role in winter rapeseed tolerance to cold stress, and Longyou-7 is slightly slower than Lenox. Our results provide a transcriptome database and candidate genes for further study of winter rapeseed cold stress.

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“…Proteins can directly affect phenotypes by controlling a series of molecular processes in plants, including signaling transduction pathways, the genic expression process, and secondary metabolic processes [ 14 ]. Proteins perform several biological functions, and their abundance depends on transcription and post-transcriptional translation [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative proteomics analysis reveals the molecular mechanism of enhanced cold tolerance through ROS scavenging in winter rapeseed (Brassica napus L.)

Zigang

Jin

et al. 2021

PLoS ONE

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Two winter rapeseed cultivars, “NS” (cold tolerant) and “NF” (cold sensitive), were used to reveal the morphological, physiological, and proteomic characteristics in leaves of plants after treatment at -4°C for 12 h(T1) and 24 h(T2), and at room temperature(T0), to understand the molecular mechanisms of cold tolerance. Antioxidant activity and osmotic adjustment ability were higher, and plasma membrane injury was less obvious, in NS than in NF under cold stress. We detected different abundant proteins (DAPs) related to cold tolerance in winter rapeseed through data-independent acquisition (DIA). Compared with NF, A total of 1,235 and 1,543 DAPs were identified in the NSs under T1 and T2, respectively. Compared with NF, 911 proteins were more abundant in NS only after cold treatment. Some of these proteins were related to ROS scavenging through four metabolic pathways: lysine degradation; phenylalanine, tyrosine, and tryptophan; flavonoid biosynthesis; and ubiquinone and other terpenoid-quinone biosynthesis. Analysis of these proteins in the four candidate pathways revealed that they were rapidly accumulated to quickly enhance ROS scavenging and improve the cold tolerance of NS. These proteins were noticeably more abundant during the early stage of cold stress, which was critical for avoiding ROS damage.

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iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

Cited by 39 publications

References 83 publications

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Transcriptome Analysis Reveals Key Cold-Stress-Responsive Genes in Winter Rapeseed (Brassica rapa L.)

Comparative proteomics analysis reveals the molecular mechanism of enhanced cold tolerance through ROS scavenging in winter rapeseed (Brassica napus L.)

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