Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae

Sun, Yibo; Zhang, Xiaojia; Zhong, Mingyu; Dong, Xue; Yu, Dongmei; Jiang, Xiaoling; Wang, Dan; Cui, Wei-Hua; Chen, Jianghua; Hu, Jin‐Yong

doi:10.1007/s11103-020-01026-7

Cited by 14 publications

(9 citation statements)

References 68 publications

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“…Of the 167 identified WD40 genes, 146 contain introns in the range of 1-36, and 21 genes have no introns. This result is consistent with Sun's identification result in Rosa chinensis (Sun et al, 2020). Introns are found in most WD40 genes, and no introns are detected in few genes.…”

Section: Discussionsupporting

confidence: 92%

“…A total of 116 proteins contain the WD40 domain, and they are classified as subclass A. The 51 remaining GbWD40 genes consist of other domains, and they are categorized as subclasses B to P. In comparison with the classification of other plants, our results on the WD40 family genes in G. biloba show similarities and differences (Feng et al, 2019;Liu et al, 2020;Sun et al, 2020). The GbWD40 protein sequence is subjected to motif analysis.…”

Section: Discussionmentioning

confidence: 88%

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Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

Zheng

Liao

et al. 2021

Not Bot Horti Agrobo

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The WD40 transcription factor family is a superfamily found in eukaryotes and implicated in regulating growth and development. In this study, 167 WD40 family genes are identified in the Ginkgo biloba genome. They are divided into 5 clusters and 16 subfamilies based on the difference analysis of a phylogenetic tree and domain structures. The distribution of WD40 genes in chromosomes, gene structures, and motifs is analyzed. Promoter analysis shows that five GbWD40 gene promoters contain the MYB binding site participating in the regulation of flavonoid metabolism, suggesting that these five genes may participate in the regulation of flavonoid synthesis in G. biloba. The correlation analysis is carried out based on FPKM value of WD40 gene and flavonoid content in 8 tissues of G. biloba. Six GbWD40 genes that may participate in flavonoid metabolism are screened. The biological functions of the WD40 family genes in G. biloba are systematically analyzed, providing a foundation for further elucidating their regulatory mechanisms. A number of WD40 candidate genes involved in the biosynthesis and metabolism of G. biloba also predicted. This study presents an important basis and direction for conducting further research on the regulatory network of flavonoid synthesis and metabolism.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 88%

Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

Zheng

Liao

et al. 2021

Not Bot Horti Agrobo

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“…In the 178 WD40 genes of potato, 3 pairs of genes were identified as tandemly duplicated, and 14 pairs of genes were related to segmental duplication ( Liu et al, 2020 ). Among of the 187 WD40 genes in rose, 11 members were identified as stemming from tandem duplication ( Sun et al, 2020 ). In the hexaploid wheat, 743 WD40 genes were identified, and 39 and 46 pairs of WD40 s were distinguished as tandem and segmental duplication genes, respectively ( Hu et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…In Solanum tuberosum , 178 StWD40 genes and in Mangifera indica , 315 MiWD40 genes were classified into 14 and 11 groups, respectively ( Liu et al, 2020 ; Tan et al, 2021 ). In Triticum aestivum , Prunus persica , Rosa chinensis , and Ginkgo biloba , 743 TaWD40 genes, 220 PpWD40 genes, 187 RcWD40 genes, and 167 GbWD40 genes were each clustered into 5 groups ( Hu et al, 2018 ; Feng et al, 2019 ; Sun et al, 2020 ; Zheng et al, 2021a , b ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L.

et al. 2022

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WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97’s localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB–bHLH–WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.

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“…COP1 is involved in photomorphogenesis of plants and plays a key role in stomatal regulation and the dehydration response [ 66 ]. COP1-like regulates many developmental processes of plants, is a repressor of plant photomorphogenesis and plays an important role in regulating fruit ripening [ 67 ]. UVR8 protein can interact with COP1, and the controlled signal cascade mediates the photomorphogenesis of UV-B radiation and improves the adaptability of plants to UV radiation [ 68 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

Gong

Liu

Chen

et al. 2022

IJMS

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As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

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Genome-wide identification of WD40 genes reveals a functional diversification of COP1-like genes in Rosaceae

Cited by 14 publications

References 68 publications

Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L.

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

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