Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

Huang, Junjun; Li, Xiaoyü; Chen, Xin; Guo, Yaru; Liang, Weihong; Wang, Hua-hua

doi:10.3390/ijms22126556

Cited by 29 publications

(21 citation statements)

References 80 publications

(111 reference statements)

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“…ATP-binding cassette (ABC) transporters are a wide and ancestral transmembrane protein family found in many natural species, which have received a lot of attention because of their multiple biological functions ( Caña-Bozada et al, 2019 ; Huang et al, 2021 ). Here, 188 tentative ABC transporter genes or fragments were screened out from the transcriptome data ( Supplementary Table 4 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn

Song

Jia

et al. 2022

Front. Plant Sci.

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Peucedanum praeruptorum Dunn is a commonly used traditional Chinese medicine that is abundant in furano- and dihydropyrano coumarins. When P. praeruptorum reaches the bolting stage, the roots gradually lignified, and the content of coumarins declines rapidly. Non-bolting has always been a decisive factor for harvesting the P. praeruptorum materials. To evaluate the amount of coumarin components in unbolted and bolted P. praeruptorum, the variations of praeruptorin A, praeruptorin B, praeruptorin E, peucedanocoumarin I, and peucedanocoumarin II were determined. Additionally, 336,505 transcripts were obtained from the comparative transcriptome data. Among them, a total of 1,573 differentially expressed genes were screened out. To identify the critical genes involved in coumarin biosynthesis, comparative transcriptomics coupled with co-expression associated analysis was conducted. Finally, coumarin biosynthesis-related eighteen candidate genes were selected for the validation of qPCR. Additionally, a phylogenetic tree and the expression profile of ATP-binding cassette (ABC) transporters were constructed. To clarify the main genes in the regulation of coumarin biosynthesis, the interaction network of the co-expression genes from thirteen modules was constructed. Current results exhibited the significant increment of praeruptorin A, praeruptorin B and praeruptorin E in the bolted P. praeruptorum. Although, peucedanocoumarin I and peucedanocoumarin II were slightly increased. Besides the content of coumarins, the essential genes involved in the coumarin biosynthesis also exhibited an overall downward trend after bolting. Three peroxidases (PRXs) involved in the production of lignin monomers had been demonstrated to be downregulated. PAL, C4H, HCT, COMT, CCoAOMT, and some ABC transporters were dramatically downregulated at the bolting stage. These results indicated that the downregulation of coumarin biosynthetic genes in the bolted P. praeruptorum ultimately reduced the formation of coumarins. However, the mechanism through which bolting indirectly affects the formation of coumarin still needs extra functional verification.

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Section: Resultsmentioning

confidence: 99%

Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn

Song

Jia

et al. 2022

Front. Plant Sci.

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“…20-25 were visualized in rose (Feng Y et al 2019). In CcABCI subfamily 3 to 7 exons were identified in Soyabean (Huang J et al 2021).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive genome-wide identification and characterization of ABC Transporter superfamily in Cajanus cajan and its expression profiling under different developmental stages in various anatomical tissues

Mall

Shah

Singh³

et al. 2023

Preprint

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Plant ATP- binding cassette (ABC) protein family is the largest multifunctional highly conserved protein superfamily that transports diverse substrates across biological membranes by the hydrolysis of ATP and is also the part of the several other biological processes like cellular detoxification, growth and development, stress biology, and signaling processes. In the agriculturally important legume crop Cajanuscajan, a genome-wide identification and characterization of the ABC gene family was carried out. A total of 159 ABC genes were identified that belong to eight canonical classes CcABCA to CcABCG and CcABCI based on the phylogenetic analysis. The number of genes was highest in CcABCG followed by CcABCC and CcABCB class. A total of 85 CcABC genes were found on 11 chromosomes and 74 were found on scaffold. Tandem duplication was the major driver of CcABC gene family expansion. The dN/dS ratio revealed the purifying selection. The phylogenetic analysis revealed class specific eight superclades which reflect their functional importance. The largest clade was found to be CcABCG which reflects their functional significance. CcABC proteins were mainly basic in nature and found to be localized in the plasma membrane.The secondary structure prediction revealed the dominance of α-helix. The canonical transmembrane and nucleotide binding domain, signature motif LSSGQ, Walker A, Walker B region and Q loop were also identified. A class-specific exon- intron pattern was also observed. In addition to core elements, different cis-acting regulatory elements like stress, hormone, and cellular responsive were also identified. Expression profiling of CcABC genes at various developmental stages of different anatomical tissues was performed and it was noticed that CcABCF3, CcABCF4, CcABCF5, CcABCG66,and CcABCI3 had the highest expression. The results of the current study endow us with the further functional analysis of Cajanus ABC in the future.

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“…The software TBtools (v1.0692) was used to draw gene structures by comparing cDNA sequences with the corresponding genomic DNA sequences of their GmAP2/ERF transporter members ( Wang et al, 2017 ; Huang et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean

Wang

Shen

et al. 2022

Front. Plant Sci.

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Drought is a major environmental constraint that causes substantial reductions in plant growth and yield. Expression of stress-related genes is largely regulated by transcription factors (TFs), including in soybean [Glycine max (L.) Merr.]. In this study, 301 GmAP2/ERF genes that encode TFs were identified in the soybean genome. The TFs were divided into five categories according to their homology. Results of previous studies were then used to select the target gene GmAP2/ERF144 from among those up-regulated by drought and salt stress in the transcriptome. According to respective tissue expression analysis and subcellular determination, the gene was highly expressed in leaves and encoded a nuclear-localized protein. To validate the function of GmAP2/ERF144, the gene was overexpressed in soybean using Agrobacterium-mediated transformation. Compared with wild-type soybean, drought resistance of overexpression lines increased significantly. Under drought treatment, leaf relative water content was significantly higher in overexpressed lines than in the wild-type genotype, whereas malondialdehyde content and electrical conductivity were significantly lower than those in the wild type. Thus, drought resistance of transgenic soybean increased with overexpression of GmAP2/ERF144. To understand overall function of the gene, network analysis was used to predict the genes that interacted with GmAP2/ERF144. Reverse-transcription quantitative PCR showed that expression of those interacting genes in two transgenic lines was 3 to 30 times higher than that in the wild type. Therefore, GmAP2/ERF144 likely interacted with those genes; however, that conclusion needs to be verified in further specific experiments.

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Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

Cited by 29 publications

References 80 publications

Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn

Comparative Transcriptomics Unveil the Crucial Genes Involved in Coumarin Biosynthesis in Peucedanum praeruptorum Dunn

Comprehensive genome-wide identification and characterization of ABC Transporter superfamily in Cajanus cajan and its expression profiling under different developmental stages in various anatomical tissues

Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean

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