Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Xia, Jichun; Wang, Dong; Peng, Yuzhou; Wang, Wenning; Wang, Qianqian; Xu, Yongsheng; Li, Tongzhou; Zhang, Kai; Li, Jiana; Xu, Xinhua

doi:10.3390/genes12070981

Cited by 13 publications

(8 citation statements)

References 77 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This result is consistent with our analysis of cis-regulatory elements and indicates that the functions of duplicate YABBY genes might have diverged during the growth and development of both B. rapa and B. oleracea. We can deduce that the duplicate YABBY genes in other Brassicaceae species might have also functionally diverged similarly to those of B. rapa or B. oleracea, as recently demonstrated in B. napus [76].…”

Section: Discussionsupporting

confidence: 66%

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

Álam

Yang

et al. 2021

Plants

View full text Add to dashboard Cite

The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.

show abstract

Section: Discussionsupporting

confidence: 66%

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

Álam

Yang

et al. 2021

Plants

View full text Add to dashboard Cite

show abstract

“…YABBYs, both C2C2 zinc finger and YABBY domain-containing TRs, are widely involved in lateral organ development in higher plants and the identification of YABBY gene family has made progress in many plants ( Lu et al, 2021 ; Xia et al, 2021 ; Yin et al, 2022 ; Zeng et al, 2022 ). However, systematic investigation of the OsYABBYs-interacting proteins have been poorly reported.…”

Section: Discussionmentioning

confidence: 99%

“…It has been reported that YABBY genes have shown functional differentiation in some species, such as Phalaenopsis orchid, Brassica napus , Cucumis sativus ( Chen et al, 2020b ; Xia et al, 2021 ; Yin et al, 2022 ), and so on. According to the clustering and expression pattern of this study, OsYABBYs also exhibited functionally diverged and were involved in different biological processes.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis

Zhang

et al. 2023

PeerJ

View full text Add to dashboard Cite

As plant-specific transcription regulators, YABBYs are involved in plant growth, development and stress responses. However, little information is available about genome-wide screening and identification of OsYABBY-interacting proteins. In this study, phylogenetic relationship, gene structure, protein structure and gene expression profile of eight OsYABBYs were carried out, all of which indicated that OsYABBYs were involved in different developmental processes and had functional differentiation. More importantly, PPI (protein-protein interaction) analysis and molecular docking simulation predicted that WUSCHEL-related homeobox (WOX) proteins might be interacting proteins of OsYABBYs. Yeast two-hybrid (Y2H) and luciferase complementation imaging assays (LCI) further confirmed that OsYABBYs (except for OsYABBY7) could interact with OsWOX3A in vitro and in vivo. In addition, OsYABBY3 and OsYABBY5 also could interact with OsWUS. Taken together, our results provided valuable information for further elucidating OsYABBYs regulation mechanism in improving rice performance.

show abstract

“…Seeking salt-stress-related genes is important work in the modern breeding of Nelumbo nucifera Gaertn. Although a number of articles on YABBY in other species have been published, there have been few reported on Nelumbo nucifera [ 11 , 35 , 36 ]. In our study, we identified nine YABBY members in lotus.…”

Section: Introductionmentioning

confidence: 99%

Identification of YABBY Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

Zhao

Zhang

Tan

et al. 2023

Plants

View full text Add to dashboard Cite

The plant-specific transcription factor family YABBY plays important roles in plant responses to biotic and abiotic stresses. Although the function of YABBY has been identified in many species, systematic analysis in lotus (Nelumbo nucifera) is still relatively lacking. The present study aimed to characterize all of the YABBY genes in lotus and obtain better insights into NnYABBYs in response to salt stress by depending on ABA signaling. Here, we identified nine YABBY genes by searching the whole lotus genome based on the conserved YABBY domain. Further analysis showed that these members were distributed on six different chromosomes and named from YABBY1 to YABBY9, which were divided into five subgroups, including YAB1, YAB2, YAB5, INO, and CRC. The analysis of cis-elements in promotors revealed that NnYABBYs could be involved in plant hormone signaling and plant responses to abiotic stresses. Quantitative real-time PCR (qRT-PCR) showed that NnYABBYs could be up-regulated or down-regulated by ABA, fluridone, and salt treatment. Subcellular localization indicated that NnYABBY4, NnYABBY5, and NnYABBY6 were mainly localized in the cell membrane and cytoplasm. In addition, the intrinsic trans-activity of NnYABBY was tested by a Y2H assay, which revealed that NnYABBY4, NnYABBY5, and NnYABBY6 are deprived of such a property. This study provided a theoretical basis and reference for the functional research of YABBY for the molecular breeding of lotus.

show abstract

Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Cited by 13 publications

References 77 publications

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

Evolutionary Analysis of the YABBY Gene Family in Brassicaceae

Comprehensive study of rice YABBY gene family: evolution, expression and interacting proteins analysis

Identification of YABBY Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

Contact Info

Product

Resources

About