Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Wan, Yuanyuan; Wang, Zhen; Xia, Jichun; Shen, Shuai; Guan, Mingwei; Zhu, Meichen; Qiao, Cailin; Sun, Fangfang; Liang, Ying; Li, Jiana; Lu, Kun; Qu, Cunmin

doi:10.3390/ijms21062209

Cited by 16 publications

(11 citation statements)

References 86 publications

(165 reference statements)

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“…These genes still retained multiple pairs of duplicate genes in this case, which also proved that polyploidy may protect genes through rapid subfunctionalization [ 42 ]. This phenomenon has also been found in another gene family in Brassica [ 43 ].…”

Section: Discussionsupporting

confidence: 73%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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Background Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis. Results In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus. Conclusions In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

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Section: Discussionsupporting

confidence: 73%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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“…The expression profiles of BnaMATE genes under heavy metal (As 3+ and Cd 2+ ) [ 83 ] and hormone (BioProject ID PRJNA608211) treatments were investigated by RNA sequencing (RNA-seq). The plant materials and heavy metal and hormone treatments were as described in previous work [ 83 , 84 , 85 ]. The expression profiles of candidate BnaMATE genes were calculated based on FPKM values and visualized as heatmaps by using HemI 1.0 [ 82 ].…”

Section: Methodsmentioning

confidence: 99%

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Qiao

Yang

Wan

et al. 2020

Plants

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The multidrug and toxic compound extrusion (MATE) protein family is important in the export of toxins and other substrates, but detailed information on this family in the Brassicaceae has not yet been reported compared to Arabidopsis thaliana. In this study, we identified 57, 124, 81, 85, 130, and 79 MATE genes in A. thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Brassica juncea, and Brassica nigra, respectively, which were unevenly distributed on chromosomes owing to both tandem and segmental duplication events. Phylogenetic analysis showed that these genes could be classified into four subgroups, shared high similarity and conservation within each group, and have evolved mainly through purifying selection. Furthermore, numerous B. napusMATE genes showed differential expression between tissues and developmental stages and between plants treated with heavy metals or hormones and untreated control plants. This differential expression was especially pronounced for the Group 2 and 3 BnaMATE genes, indicating that they may play important roles in stress tolerance and hormone induction. Our results provide a valuable foundation for the functional dissection of the different BnaMATE homologs in B. napus and its parental lines, as well as for the breeding of more stress-tolerant B. napus genotypes.

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“…The rapeseed cultivar “Zhongshuang 11 (ZS11)” were used as plant material. To investigate the expression pattern in response to heavy metal stress treatments, the expression profiles of BnaTIFYs were further analyzed using published RNA-seq dataset underAs 3+ and Cd 2+ stress [ 52 ]. The plant materials and treatments were as described previous [ 52 ].…”

Section: Methodsmentioning

confidence: 99%

“…To investigate the expression pattern in response to heavy metal stress treatments, the expression profiles of BnaTIFYs were further analyzed using published RNA-seq dataset underAs 3+ and Cd 2+ stress [ 52 ]. The plant materials and treatments were as described previous [ 52 ]. All the relative expression levels of TIFYs were calculated and normalized as FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) with TopHat and Cufflinks [ 53 ].…”

Section: Methodsmentioning

confidence: 99%

“…3.0 (Takara, Dalian, China). We subsequently performed qRT-PCR analysis using SYBR Premix Ex Taq II (Takara, Dalian, China) on a Bio-Rad CFX96 Real Time System (Bio-Rad Laboratories, Hercules, CA, USA) as previously described [ 52 ]. Finally, TIFY gene expression levels were normalized using a reference gene BnACTIN7 (EV116054) [ 55 ] via the 2 −∆∆Ct method.…”

Section: Methodsmentioning

confidence: 99%

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Genome-Wide Identification of the TIFY Gene Family in Brassiceae and Its Potential Association with Heavy Metal Stress in Rapeseed

Sun

Chen

Zhang

et al. 2022

Plants

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The TIFY gene family plays important roles in various plant biological processes and responses to stress and hormones. The chromosome-level genome of the Brassiceae species has been released, but knowledge concerning the TIFY family is lacking in the Brassiceae species. The current study performed a bioinformatics analysis on the TIFY family comparing three diploid (B. rapa, B. nigra, and B. oleracea) and two derived allotetraploid species (B. juncea, and B. napus). A total of 237 putative TIFY proteins were identified from five Brassiceae species, and classified into ten subfamilies (six JAZ types, one PPD type, two TIFY types, and one ZML type) based on their phylogenetic relationships with TIFY proteins in A. thaliana and Brassiceae species. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the TIFY family genes during the process of polyploidization, and most of these TIFY family genes (TIFYs) were subjected to purifying selection after duplication based on Ka/Ks values. The spatial and temporal expression patterns indicated that different groups of BnaTIFYs have distinct spatiotemporal expression patterns under normal conditions and heavy metal stresses. Most of the JAZIII subfamily members were highest in all tissues, but JAZ subfamily members were strongly induced by heavy metal stresses. BnaTIFY34, BnaTIFY59, BnaTIFY21 and BnaTIFY68 were significantly upregulated mostly under As3+ and Cd2+ treatment, indicating that they could be actively induced by heavy metal stress. Our results may contribute to further exploration of TIFYs, and provided valuable information for further studies of TIFYs in plant tolerance to heavy metal stress.

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Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Cited by 16 publications

References 86 publications

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

A Genome-Wide Survey of MATE Transporters in Brassicaceae and Unveiling Their Expression Profiles under Abiotic Stress in Rapeseed

Genome-Wide Identification of the TIFY Gene Family in Brassiceae and Its Potential Association with Heavy Metal Stress in Rapeseed

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