Tumorous Stem Development of Brassica Juncea: A Complex Regulatory Network of Stem Formation and Identification of Key Genes in Glucosinolate Biosynthesis

Li, Mengyao; Xie, Fangjie; Li, Jie; Sun, Bo; Luo, Yunbo; Zhang, Yong; Wang, Yan; Zhang, Fen; Zhang, Yunting; Lin, Yuanxiu; Wang, Xiaorong; Tang, Haoru

doi:10.3390/plants9081006

Cited by 8 publications

(6 citation statements)

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“…Total genomic DNA was extracted from the frozen leaves following a modified CTAB protocol [18]. The DNA samples were then subjected to quality and quantity checks using 1% agarose gel electrophoresis and spectrophotometric methods measured by a Nanodrop ND1000 spectrophotometer [19]. High-quality cp DNA was used to prepare a library with an insert size of 350 bp, which was then sequenced on an Illumina Novaseq platform [20] at Nanjing Genepioneer Biotechnologies Inc. (Nanjing, China).…”

Section: Dna Extraction and Sequencingmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants.

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Section: Dna Extraction and Sequencingmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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“…The fleshy stems of the stem lettuce ‘Yonganhong’ at four expansion stages (S1, S2, S3, and S4) were fixed in 50 mL 50% FAA fixative and placed at 4°C for 24 h. Then, the treated samples were embedded in paraffin and stained with safranin O-fast green reagent referring to previous methods ( Li et al., 2020 ). The anatomical structure during the process of fleshy stem expansion was observed and recorded with CaseViewer (version 7.3).…”

Section: Methodsmentioning

confidence: 99%

“…A variety of metabolites and genes have been confirmed to participate in the expansion process of plant organs (root, stem). During mustard stem development process, most differentially expressed genes (DEGs) were identified to involve in the synthesis, accumulation, and metabolism process of sugars, starch, and storage proteins ( Li et al., 2020 ). A large number of genes have been identified to involve in the process of rhizome development.…”

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confidence: 99%

Combined analysis of the transcriptome and metabolome provides insights into the fleshy stem expansion mechanism in stem lettuce

Huang

Li²,

Liu³

et al. 2022

Front. Plant Sci.

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As a stem variety of lettuce, the fleshy stem is the main product organ of stem lettuce. The molecular mechanism of fleshy stem expansion in stem lettuce is a complex biological process. In the study, the material accumulation, gene expression, and morphogenesis during fleshy stem expansion process were analyzed by the comparative analysis of metabolome, transcriptome and the anatomical studies. The anatomical studies showed that the occurrence and activity of vascular cambium mainly led to the development of fleshy stems; and the volume of pith cells gradually increased and arranged tightly during the expansion process. A total of 822 differential metabolites and 9,383 differentially expressed genes (DEGs) were identified by the metabolomics and transcriptomics analyses, respectively. These changes significantly enriched in sugar synthesis, glycolysis, and plant hormone anabolism. The expression profiles of genes in the sugar metabolic pathway gradually increased in fleshy stem expansion process. But the sucrose content was the highest in the early stage of fleshy stem expansion, other sugars such as fructose and glucose content increased during fleshy stem expansion process. Plant hormones, including IAA, GA, CTK, and JA, depicted important roles at different stem expansion stages. A total of 1,805 DEGs were identified as transcription factors, such as MYB, bHLH, and bZIP, indicating that these transcription factor families might regulate the fleshy stems expansion in lettuce. In addition, the expression patterns identified by qRT-PCR were consistent with the expression abundance identified by the transcriptome data. The important genes and metabolites identified in the lettuce fleshy stem expansion process will provide important information for the further molecular mechanism study of lettuce fleshy stem growth and development.

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“…Transcriptome analyses by RNA sequencing (RNA-seq) have been conducted to explore the complex genetic mechanism behind the formation of tuberous organs in brassica and many other crops; radish (Mitsui et al, 2015;Xie et al, 2018;Yu et al, 2015Yu et al, , 2016, turnip (Li et al, 2015;Liu et al, 2019), sweet potato (Dong et al, 2019), tumorous stem mustard (Li et al, 2020;Sun et al, 2012), Chinese yam (Zhou et al, 2020), Rehmania glutinosa (Sun et al, 2015) and Panax notoginseng (Li et al, 2019). Consequently, they revealed the differential expression of certain potential genes, which are highly involved in several biological processes, including cell wall organization, cell division, carbohydrate metabolism, signal transduction and transcription factors (TFs).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis during tuberous stem formation in Kohlrabi (B. oleracea var. gongylodes) at early growth periods (seedling stages)

Nuruzzaman

Sato

Okamoto

et al. 2022

Physiologia Plantarum

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Tuberous stem of kohlrabi is an important agronomic trait, however, the molecular basis of tuberization is poorly understood. To elucidate the tuberization mechanism, we conducted a comparative transcriptomic analysis between kohlrabi and broccoli at 10 and 20 days after germination (DAG) as tuberous stem initiated between these time points. A total of 5580 and 2866 differentially expressed transcripts (DETs) were identified between genotypes (kohlrabi vs. broccoli) and growth stages (10 DAG vs. 20 DAG), respectively, and most of the DETs were down-regulated in kohlrabi. Gene ontology (GO) and KEGG pathway enrichment analyses showed that the DETs between genotypes are involved in cell wall loosening and expansion, cell cycle and division, carbohydrate metabolism, hormone transport, hormone signal transduction and in several transcription factors. The DETs identified in those categories may directly/indirectly relate to the initiation and development of tuberous stem in kohlrabi. In addition, the expression pattern of the hormone synthesis related DETs coincided with the endogenous IAA, IAAsp, GA, ABA, and tZ profiles in kohlrabi and broccoli seedlings, that were revealed in our phytohormone analysis. This is the first report on comparative transcriptome analysis for tuberous stem formation in kohlrabi at early growth periods. The resulting data could provide significant insights into the molecular mechanism underlying tuberous stem development in kohlrabi as well as in other tuberous organ forming crops.

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Tumorous Stem Development of Brassica Juncea: A Complex Regulatory Network of Stem Formation and Identification of Key Genes in Glucosinolate Biosynthesis

Cited by 8 publications

References 58 publications

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Combined analysis of the transcriptome and metabolome provides insights into the fleshy stem expansion mechanism in stem lettuce

Comparative transcriptome analysis during tuberous stem formation in Kohlrabi (B. oleracea var. gongylodes) at early growth periods (seedling stages)

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