Dataset Information

The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis.

ABSTRACT: Background:The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat. Objective:To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and its two progenitors using updated genome information provided here. Results:In total, 63, 13 and 17 TIFY proteins were identified in wheat, Triticum urartu and Aegilops tauschii respectively. Phylogenetic analysis clustered them into 18 groups with 14 groups possessing A, B and D copies in wheat, demonstrating the completion of the genome as well as the two rounds of allopolyploidization events. Gene structure, conserved protein motif and cis-regulatory element divergence of A, B, D homoeologous copies were also investigated to gain insight into the evolutionary conservation and divergence of homoeologous genes. Furthermore, the expression profiles of the genes were detected using the available RNA-seq and the expression of 4 drought-responsive candidates was further validated through qRT-PCR analysis. Finally, the co-expression network was constructed and a total of 22 nodes with 121 edges of gene pairs were found. Conclusion:This study systematically reported the characteristics of the wheat TIFY family, which ultimately provided important targets for further functional analysis and also facilitated the elucidation of the evolution mechanism of TIFY genes in wheat and more.

SUBMITTER: Xie S

PROVIDER: S-EPMC7235398 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis.

Xie Songfeng S Cui Licao L Lei Xiaole X Yang Guang G Li Jun J Nie Xiaojun X Ji Wanquan W

Current genomics 20190801 5

<h4>Background</h4>The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat.<h4>Objective</h4>To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and i ...[more]

PMID: 32476994

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Project description:BackgroundThe trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives.ResultsWe identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon, and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses.ConclusionsIn this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs.

Dataset Information

The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis.

Publications

The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis.

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