Genome-wide identification and characterization of TCP family genes in <i>Brassica juncea</i> var. tumida

He, Jian‐Jun; He, Xu; Chang, Ping‐An; Jiang, Huaizhong; Gong, Daping; Sun, Quan

doi:10.7717/peerj.9130

Cited by 13 publications

(10 citation statements)

References 91 publications

(71 reference statements)

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“…Owing to the development, duplications, and divergence of TCP genes, the gymnosperms and angiosperms plants possess bigger TCP gene families containing more than ten TCP members ( Martín-Trillo and Cubas, 2010 ). Over the past few years, TCP gene families have been reported in various crop plants such as Arabidopsis thaliana ( Yao et al, 2007 ), Moso bamboo ( Liu et al, 2018 ), sweet potato ( Ren et al, 2021 ), cucumber ( Wen et al, 2020 ), rice ( Yao et al, 2007 ), Brassica rapa ( Du et al, 2017 ); Brassica juncea ( He et al, 2020 ); and cotton ( Ma et al, 2014 ; Yin et al, 2018 ), etc. To our best knowledge, the TCP gene family has not been fully characterized in the rapeseed genome.…”

Section: Discussionmentioning

confidence: 99%

“…rapa) ( Du et al, 2017 ); 63 TCP members in Brassica juncea var. tumida ( He et al, 2020 ), 73 TCP members in allotetraploid cotton ( Gossypium hirsutum L.) ( Yin et al, 2018 ), etc. Several studies have shown that TCP genes play significant roles in plant growth and developmental processes, including trichome formation ( Wang et al, 2013 ), seed germination ( Zhang et al, 2019 ), petal development ( van Es et al, 2018 ), floral development ( Li et al, 2019 ), shoot branching ( Braun et al, 2012 ), and leaf anatomical morphology ( Ren et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

et al. 2021

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TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

et al. 2021

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“…The formation and development of bulblet is a complex process regulated by a series of transcription factors (Gao et al 2018 ; Moreno-Pachon et al 2016 ). The teosinte branched1/cycloidea/proliferating cell factor1 (TCP) is a special transcription factor family involved in activation or inhibition cell proliferation and related to branching, leaf development, and germination (He et al 2020 ). TCP transcription factors have been reported in many plant species, such as 24 TCP in Arabidopsis (Li 2015 ), 39 TCP in Brassica rapa L .…”

Section: Discussionmentioning

confidence: 99%

“…During the tuber swollen stage of Brassica juncea var. tumida, the expression of 6 BjTCP genes were significantly upregulated (He et al 2020 ). The root hair, density, and stem trichome were increased when the GbTCP5 gene in transgenic Arabidopsis was overexpressed (Wang et al 2020b ).…”

Section: Discussionmentioning

confidence: 99%

Hydrogen-rich water promotes the formation of bulblets in Lilium davidii var. unicolor through regulating sucrose and starch metabolism

Hou

Wang

et al. 2021

Planta

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Main conclusion HRW increased the content of starch and sucrose via regulating a series of sucrose and starch synthesis genes, which induced the formation of bulblets and adventitious roots of Lilium davidii var. unicolor. Abstract Hydrogen gas (H 2 ), as a signaling molecule, has been reported to be involved in plant growth and development. Here, the effect of hydrogen-rich water (HRW) on the formation of bulblets and adventitious roots in the scale cuttings of Lilium davidii var. unicolor and its mechanisms at the molecular levels were investigated. The results revealed that compared with distilled water treatment (Con), the number of bulblets and adventitious roots were significantly promoted by different concentrations of HRW treatment. Treatment with 100% HRW obtained the most positive effects. RNA sequencing (RNA-seq) analysis found that compared with Con, a total of 1702 differentially expressed genes (DEGs, upregulated 552 DEGs, downregulated 1150 DEGs) were obtained under HRW treatment. The sucrose and starch metabolism, cysteine and methionine metabolism and phenylalanine metabolism were significantly enriched in the analysis of the Kyoto encyclopedia of genes and genomes (KEGG). In addition, the genes involved in carbohydrate metabolism were significantly upregulated or downregulated (upregulated 22 DEGs, downregulated 15 DEGs), indicating that starch and sucrose metabolism held a central position. The expressions of 12 DEGs were identified as coding for key enzymes in metabolism of carbohydrates was validated by qPCR during bulblet formation progress. RNA-seq analysis and expression profiles indicated that the unigene levels such as glgc, Susy, otsA and glgP, BMY and TPS were well correlated with sucrose and starch metabolism during HRW-induced bulblet formation. The change of key enzyme content in starch and sucrose metabolism pathway was explored during bulblet formation in Lilium under HRW treatment. Meanwhile, compared with Con, 100% HRW treatment increased the levels of sucrose and starch, and decreased the trehalose content, which were agreed with the expression pattern of DEGs related to the biosynthesis pathway of sucrose, starch and trehalose. Therefore, this study suggested that HRW could promote the accumulation of sucrose and starch contents in mother scales, and decreased the trehalose content, this might provide more energy for bulblet formation. Supplementary Information The online version contains supplementary material available at 10.1007/s00425-021-03762-6.

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“…juncea var. tumida has a larger genome, which is an allotetraploid (AABB), resulting from the hybridization between diploid ancestors of B. rapa (AA) and B. nigra (BB), followed by spontaneous chromosome doubling ( He et al, 2020 ). Therefore, the number of NAC genes in B .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida

Jiang

Sun

Wang

et al. 2021

PeerJ

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Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.

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Genome-wide identification and characterization of TCP family genes in Brassica juncea var. tumida

Cited by 13 publications

References 91 publications

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

Hydrogen-rich water promotes the formation of bulblets in Lilium davidii var. unicolor through regulating sucrose and starch metabolism

Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida

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