Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)

Yue, Hong; Shu, Duntao; Wang, Meng; Xing, Guangwei; Zhan, Haoshuang; Du, Xianghong; Song, Weining; Nie, Xiaojun

doi:10.3390/genes9020070

Cited by 51 publications

(47 citation statements)

References 67 publications

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“…Contribution of homoeolog expression dominance in facilitating selection of glucosinolate and lipid metabolism genes was also reported in the vegetable-use and oil-use sub-varieties of Brassica juncea 51 . In cotton and wheat, alterations of expression patterns among homoeologs under variation in stress conditions, tissues, and developmental stages have also been documented [52][53][54][55][56][57] . Given the consequences of unequal expression to the natural gene selections in polyploids, it is important to understand the genetic basis of valuable traits with respect to the homology and homoeology perspectives for the success of selective breeding programs.…”

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confidence: 97%

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat

Erdayani

Nagarajan

Grant

et al. 2020

Sci Rep

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Heat Shock Protein 101 (HSP101), the homolog of Caseinolytic Protease B (CLPB) proteins, has functional conservation across species to play roles in heat acclimation and plant development. In wheat, several TaHSP101/CLPB genes were identified, but have not been comprehensively characterized. Given the complexity of a polyploid genome with its phenomena of homoeologous expression bias, detailed analysis on the whole TaCLPB family members is important to understand the genetic basis of heat tolerance in hexaploid wheat. In this study, a genome-wide analysis revealed thirteen members of TaCLPB gene family and their expression patterns in various tissues, developmental stages, and stress conditions. Detailed characterization of TaCLPB gene and protein structures suggested potential variations of the sub-cellular localization and their functional regulations. We revealed homoeologous specific variations among TaCLPB gene copies that have not been reported earlier. A study of the Chromosome 1 TaCLPB in four wheat genotypes demonstrated unique patterns of the homoeologous gene expression under moderate and extreme heat treatments. The results give insight into the strategies to improve heat tolerance by targeting one or some of the TaCLPB genes in wheat.

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confidence: 97%

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat

Erdayani

Nagarajan

Grant

et al. 2020

Sci Rep

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“…NORMAL=1). In a recently study, a total of 46 HD-Zip genes were identified in wheat by a genomewide bioinformatic survey [35]. In this study, we further identified 67 additional HD-Zip genes in wheat latest genome and extended the total member to 113.…”

Section: Identification Of the Hd-zip Gene Family In Wheatmentioning

confidence: 87%

Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis

Chen

et al. 2020

Preprint

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Background: Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. Results: To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. Conclusions: Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.

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“…We kept predicted proteins with both identity and coverage higher than 0.5. According to previous homologous gene identification methods 25, 26 , we also we performed pairwise alignments for all protein sequence, using CD-HIT 27 with the parameters of identity > 90% and coverage > 70%. In this way Coronavirus proteins are clustered into 322 unified gene clusters.…”

Section: Methodsmentioning

confidence: 99%

A database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale

Zhu

Meng

2020

Preprint

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The recent outbreak of a new zoonotic origin Coronavirus has ring the bell for the potential spread of epidemic Coronavirus crossing the species. With the urgent needs to assist the control of the Coronavirus spread and to provide valuable scientific information, we developed a coronavirus database (CoVdb), an online genomics and proteomics analysis platform. Based on public available coronavirus genomic information, the database annotates the genome of every strain and identifies 780 possible ORFs of all strains available in Genebank. In addition, the comprehensive evaluation of all the published genomes of Coronavirus strains, including population genetics analysis, functional analysis and structural analysis on a historical and global scale were presented in the CoVdb. In the database, the researcher can easily obtain the basic information of a Coronavirus gene with the distribution of the gene among strains, conserved or high mutation regions, possible subcellular location and topology of the gene. Moreover, sliding windows for population genetics analysis results is provided, thereby facilitating genetics and evolutional analysis at the genomic level. CoVdb can be accessed freely at http://covdb.popgenetics.net.

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Genome-Wide Identification and Expression Analysis of the HD-Zip Gene Family in Wheat (Triticum aestivum L.)

Cited by 51 publications

References 67 publications

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat

Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat

Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis

A database resource for Genome-wide dynamics analysis of Coronaviruses on a historical and global scale

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