Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (<i>Setaria italica</i>L.)

Chai, Wenxiang; Si, Weina; Ji, Wei; Qin, Qianqian; Zhao, Manli; Jiang, Haiyang

doi:10.1155/2018/8457614

Cited by 29 publications

(17 citation statements)

References 60 publications

(66 reference statements)

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“…Numerous reports have revealed that HD-Zip genes were involved in response to a variety of abiotic stresses in different plant species, such as foxtail millet [54], tea plant [22], wheat [21], and potato [23]. In the present study, the expression levels of over 75% SiHDZ genes were found to be affected by drought or salinity stresses based on transcriptome data and qRT-PCR results.…”

Section: Discussionmentioning

confidence: 49%

“…In this study, a total of 45 SiHDZ genes were identified from the sesame genome (Additional file 2: Table S1). The number of HDZ members in sesame was comparable to that of potato (43) [23], wheat (46) [21], foxtail millet ( Setaria italica ) (47) [54], rice (48) [14, 15], and Arabidopsis (48) [6], more than tea plant (33) [22], but less than maize (55) [17] and cassava (57) [20]. These findings suggested that the number of HD-Zip genes is not correlated with genome size of these plant species, which may partly result from tandem duplication and segmental duplication.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

et al. 2019

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Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

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Section: Discussionmentioning

confidence: 49%

Section: Discussionmentioning

confidence: 99%

Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

et al. 2019

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“…All NtHD-Zip I proteins contained the α-helix and coil structure [49]. Most NtHD-Zip I members shared a similar three-dimensional structure, especially for those clustered in the same clade.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

Bai

Feng

et al. 2019

Genes

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The homeodomain-leucine zipper (HD-Zip) gene family, whose members play vital roles in plant growth and development, and participate in responding to various stresses, is an important class of transcription factors currently only found in plants. Although the HD-Zip gene family, especially the HD-Zip I subfamily, has been extensively studied in many plant species, the systematic report on HD-Zip I subfamily in cultivated tobacco (Nicotiana tabacum) is lacking. In this study, 39 HD-Zip I genes were systematically identified in N. tabacum (Nt). Interestingly, that 64.5% of the 31 genes with definite chromosome location information were found to originate from N. tomentosoformis, one of the two ancestral species of allotetraploid N. tabacum. Phylogenetic analysis divided the NtHD-Zip I subfamily into eight clades. Analysis of gene structures showed that NtHD-Zip I proteins contained conserved homeodomain and leucine-zipper domains. Three-dimensional structure analysis revealed that most NtHD-Zip I proteins in each clade, except for those in clade η, share a similar structure to their counterparts in Arabidopsis. Prediction of cis-regulatory elements showed that a number of elements responding to abscisic acid and different abiotic stresses, including low temperature, drought, and salinity, existed in the promoter region of NtHD-Zip I genes. The prediction of Arabidopsis ortholog-based protein–protein interaction network implied that NtHD-Zip I proteins have complex connections. The expression profile of these genes showed that different NtHD-Zip I genes were highly expressed in different tissues and could respond to abscisic acid and low-temperature treatments. Our study provides insights into the evolution and expression patterns of NtHD-Zip I genes in N. tabacum and will be useful for further functional characterization of NtHD-Zip I genes in the future.

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“…Compared with HD-Zip III proteins, HD-Zip IV proteins lack the C-terminal MEKHLA motif, but contain the PAS domain, which may be involved in the circadian clock and signal transduction (Mukherjee & Bürglin, 2006; Hefti et al, 2004). To date, many HD-Zip genes have been identified, and many attempts have been made to elucidate the functions of various HD-Zip genes in several species, such as Arabidopsis thaliana (Henriksson, 2005; Nakamura et al, 2006; Ciarbelli et al, 2008), rice ( Oryza sativus ) (Agalou et al, 2008), maize ( Zea mays ) (Javelle et al, 2011), tomato ( Solanum lycopersicum ) (Zhang et al, 2014a; Zhang et al, 2014b), Brassica rapa (Khan et al, 2018), cotton ( Gossypium hirsutum ) (He et al, 2018), soybean ( Glycine max ) (Chen et al, 2014), foxtail millet ( Setaria italica ) (Chai et al, 2018), sunflower ( Helianthus annuus ) (Manavella et al, 2010; Dezar et al, 2011), poplar ( Populus trichocarpa ) (Hu et al, 2012), grape ( Vitis vinifera ) (Jiang et al, 2014), pear ( Pyrus betulifolia ) (Wang et al, 2015) and peach ( Prunus persica ) (Zhang et al, 2014a; Zhang et al, 2014b).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume

Zheng

Zhuo

et al. 2019

PeerJ

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The homeodomain-leucine zipper (HD-Zip) gene family, a group of plant-specific transcriptional factors (TFs), participates in regulating growth, development, and environmental responses. However, the characteristics and biological functions of HD-Zip genes in Prunus mume, which blooms in late winter or early spring, have not been reported. In this study, 32 HD-Zip genes, named PmHB1–PmHB32 based on their chromosomal positions, were identified in the genome of P. mume. These genes are distributed among seven chromosomes and are phylogenetically clustered into four major groups. Gene structure and motif composition were mostly conserved in each group. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolution of the genes, which maintained the function of this family. MicroRNA target site prediction indicated that the genes of the HD-Zip III subfamily may be regulated by miR165/166. Expression pattern analysis showed that the 32 genes were differentially expressed across five different tissues (leaf, flower bud, stem, fruit, and root) and at different stages of stem and leaf-bud development, suggesting that 10 of the genes may play important roles in stem development. Protein–protein interaction predictions showed that the subfamily III genes may regulate vascular development and shoot apical meristem (SAM) maintenance. Promoter analysis showed that the HD-Zip III genes might be involved in responses to light, hormones, and abiotic stressors and stem development. Taken together, our results provide an overview of the HD-Zip family in P. mume and lay the foundation for the molecular breeding of woody ornamental plants.

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Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (Setaria italicaL.)

Cited by 29 publications

References 60 publications

Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

Genome-Wide Identification and Expression Analysis of HD-ZIP I Gene Subfamily in Nicotiana tabacum

Genome-wide identification, characterization and expression analysis of the HD-Zip gene family in the stem development of the woody plant Prunus mume

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