EfGD: the <i>Erianthus fulvus</i> genome database

Qian, Zhenfeng; Li, Xuzhen; He, Lili; Gu, Shujie; Shen, Qingqing; Rao, Xibing; Zhang, Rongqiong; Di, Yining; Xie, Li; Wang, Xianhong; Chen, Shuying; Dong, Yang; Li, Fusheng

doi:10.1093/database/baac076

Cited by 3 publications

(6 citation statements)

References 40 publications

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“…In a previous study, we uncovered the cold stress-induced gene EfDREB1A in E. fulvus [ 27 ]. To further investigate the AP2/ERF family in E. fulvus , a total of 145 EfAP2/ERF genes ( Table S1 ) were identified from the E. fulvus genome database [ 41 ]. The number of EfAP2/ERF genes in E. fulvus was close to that in Arabidopsis (146, genome size: 125 Mb) [ 7 ], rice (163, genome size: 466 Mb) [ 6 ], and sorghum (126, genome size: 750 Mb) [ 28 ].…”

Section: Discussionmentioning

confidence: 99%

“…The number of EfAP2/ERF genes in E. fulvus was close to that in Arabidopsis (146, genome size: 125 Mb) [ 7 ], rice (163, genome size: 466 Mb) [ 6 ], and sorghum (126, genome size: 750 Mb) [ 28 ]. Due to the small size of the genome of E. fulvus (chromosome: 2n = 20; genome size: 0.9 Gb) [ 41 ], the number of EfAP2/ERF genes was fewer than that in S. spontaneum (218, genome size: 3.36 Gb) [ 8 ], and maize (292, genome size: 2.3 Gb) [ 11 ]. These results suggest that the number of AP2/ERF family genes in different plants varies due to species specificity and variations in genome size.…”

Section: Discussionmentioning

confidence: 99%

“…The genome sequences and sequence information of E. fulvus were downloaded from the Erianthus fulvus Genome Database (EfGD) ( (accessed on 5 October 2021)) [ 41 ]. Gene family identification and analysis were performed with the Docker image tool (OmicsClass/Gene-family V1.0.1, builed by OmicsClass (Beijing, China)).…”

Section: Methodsmentioning

confidence: 99%

“…Then, the interaction networks of EfAP2/ERF proteins were identified based on the orthologous genes between E. fulvus and Arabidopsis using STRING ( (accessed on 4 May 2022)) software and visualized using Cytoscape v3.8.2 ( (accessed on 7 May 2022)) software. To identify the expression pattern of EfAP2/ERF genes, the RNA-seq expression data (FPKM value) of E. fulvus ‘99-1’, including three tissues (root, stem, and leaf) under low temperature (4 °C) stress (0, 24, and 72 h), were obtained from the EfGD [ 41 ]. The heatmap of EfAP2/ERF genes was constructed using TBtools software.…”

Section: Methodsmentioning

confidence: 99%

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Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

Qian

Rao

Zhang

et al. 2023

IJMS

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The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

Qian

Rao

Zhang

et al. 2023

IJMS

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“…Genomic data, protein files, CDS files, and gff3 files of E. fulvus were downloaded from the EfGD: E. fulvus Genome Database ( ) (accessed on 25 August 2022) online website [ 28 ]. The genomes of Arabidopsis thaliana (GenBank: GCA_000001735.2), Sorghum bicolor (GenBank: GCA_000003195.3), Miscanthus iutarioriparius (GenBank: GCA_904845875.1), Oryza sativa (GenBank: GCA_001433935.1), and Saccharum spontaneum (GenBank: GCA_022457205.1) with gff3 files were downloaded from NCBI.…”

Section: Methodsmentioning

confidence: 99%

Bioinformatics Analysis of WRKY Family Genes in Erianthus fulvus Ness

Chen

et al. 2022

Genes

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One of the most prominent transcription factors in higher plants, the WRKY gene family, is crucial for secondary metabolism, phytohormone signaling, plant defense responses, and plant responses to abiotic stresses. It can control the expression of a wide range of target genes by coordinating with other DNA-binding or non-DNA-binding interacting proteins. In this study, we performed a genome-wide analysis of the EfWRKY genes and initially identified 89 members of the EfWRKY transcription factor family. Using some members of the OsWRKY transcription factor family, an evolutionary tree was built using the neighbor-joining (NJ) method to classify the 89 members of the EfWRKY transcription factor family into three major taxa and one unclassified group. Molecular weights ranged from 22,614.82 to 303,622.06 Da; hydrophilicity ranged from (−0.983)–(0.159); instability coefficients ranged from 40.97–81.30; lipid coefficients ranged from 38.54–91.89; amino acid numbers ranged from 213–2738 bp; isoelectric points ranged from 4.85–10.06. A signal peptide was present in EfWRKY41 but not in the other proteins, and EfWRK85 was subcellularly localized to the cell membrane. Chromosome localization revealed that the WRKY gene was present on each chromosome, proving that the conserved pattern WRKYGQK is the family’s central conserved motif. Conserved motif analysis showed that practically all members have this motif. Analysis of the cis-acting elements indicated that, in addition to the fundamental TATA-box, CAAT-box, and light-responsive features (GT1-box), there are response elements implicated in numerous hormones, growth regulation, secondary metabolism, and abiotic stressors. These results inform further studies on the function of EfWRKY genes and will lead to the improvement of sugarcane.

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Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus

Rao,

Qian,

Xie

et al. 2023

Genes

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MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.

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EfGD: the Erianthus fulvus genome database

Cited by 3 publications

References 40 publications

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

Bioinformatics Analysis of WRKY Family Genes in Erianthus fulvus Ness

Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus

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