Dataset Information

Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis.

ABSTRACT: ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.

SUBMITTER: Niu H

PROVIDER: S-EPMC8462724 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis.

Niu Hongli H Xia Pengliang P Hu Yifeng Y Zhan Chuang C Li Yiting Y Gong Shuangjun S Li Yan Y Ma Dongfang D

PloS one 20210924 9

ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided ...[more]

PMID: 34559835

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Project description:BackgroundThe zinc finger-homeodomain (ZF-HD) transcription factor family is widely involved in regulating plant growth and fruit filling, as well as responding to various abiotic stress. Rapeseed (Brassica napus L.), the second largest oil-producing crop in the world, is an annual or biennial herb of Brassica in Cruciferae. However, there is currently no systematic study on the evolutionary relationship and stress response of ZF-HD transcription factors in rapeseed.ResultsIn this study, 60 ZF-HD genes in B. napus (BnZHDs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these BnZHD genes were systematically analyzed. These 60 BnZHD members were divided into seven groups. According to the phylogenetic tree and repetitive events, subfamilies MIF, and V may have undergone stronger expansions during the evolutionary process. Interestingly, segmental duplications may have a more important contribution, which distinguishes them from other dicotyledon plants. To further investigate the evolutionary relationship of the ZF-HD family, we constructed eleven comparative genomic maps of homologous genes between rapeseed and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression pattern of 15 BnZHD genes from different subfamilies under different tissues, fruit developmental stages, and different abiotic stress were analyzed. The expression profile from real-time quantitative PCR analysis showed different expression patterns of BnZHD gene in B. napus. We found that certain BnZHD genes are preferentially expressed in specific tissues of B. napus, while most genes are expressed in multiple tissues. For example, BnZHD37, BnZHD53, and BnZHD55 may be sensitive to different hormones. Under different stresses, the expression of BnZHD3, BnZHD4, BnZHD7, BnZHD38, BnZD45, and BnZHD53 significantly increased in roots, stems, and leaves within 24 h. These genes may play important roles in the growth, development, and environmental adaptation of rapeseed.ConclusionsThese findings provide a basis for a comprehensive understanding of the ZF-HD family in rapeseed, which will provide information for further research on the functional characteristics of the BnZHD genes.

Project description:Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.

Dataset Information

Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis.

Publications

Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis.

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