Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)

Gong, Xin; Zhao, Liangyi; Song, Xiaofei; Lin, Zekun; Gu, Bingjie; Yan, Jinxuan; Zhang, Shaoling; Tao, Shutian; Huang, Xiaosan

doi:10.1186/s12870-019-1760-8

Cited by 53 publications

(32 citation statements)

References 96 publications

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“…There were extensive variations in gene length, predicted protein molecular weight, and protein isoelectric point, whereas the gene structures were relatively conserved in the NAC gene family [23]. The NAC members in the same subgroups might have similar exon/intron structures and positions, indicating that these members were closely related and might have similar functions, consistent with previous studies [47,48]. However, there were a few differences between the members in the same subgroup, such as the size, relative location and number of exons.…”

Section: Discussionsupporting

confidence: 80%

Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Shan

Yang

et al. 2019

Biomolecules

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NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

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Section: Discussionsupporting

confidence: 80%

Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Shan

Yang

et al. 2019

Biomolecules

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“…These results suggested that whole-genome duplication events resulted in the expansion of the NAC family in C. songorica . NAC genes in pear undergo purification selection and positive selection while only undergoing purification selection in cotton [ 49 , 50 ]. In this study, we analyzed the evolutionary pressure between CsNAC duplicated genes (Cs-Cs) and found that the Ka/Ks ratios of all NAC duplicated genes were less than 1, indicating that NAC genes underwent purifying selection in the C. songorica genome ( Figure 3 d; Table S3 ).…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica

Zong

et al. 2020

Genes

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Plant-specific NAC (NAM, ATAF, CUC) transcription factor (TF) family plays important roles in biological processes such as plant growth and response to stress. Nevertheless, no information is known about NAC TFs in Cleistogenes songorica, a prominent xerophyte desert grass in northwestern China. In this study, 162 NAC genes were found from the Cleistogenes songorica genome, among which 156 C. songoricaNAC (CsNAC) genes (96.3%) were mapped onto 20 chromosomes. The phylogenetic tree constructed by CsNAC and rice NAC TFs can be separated into 14 subfamilies. Syntenic and Ka/Ks analyses showed that CsNACs were primarily expanded by genomewide replication events, and purifying selection was the primary force driving the evolution of CsNAC family genes. The CsNAC gene expression profiles showed that 36 CsNAC genes showed differential expression between cleistogamous (CL) and chasmogamous (CH) flowers. One hundred and two CsNAC genes showed differential expression under heat, cold, drought, salt and ABA treatment. Twenty-three CsNAC genes were commonly differentially expressed both under stress responses and during dimorphic floret development. Gene Ontology (GO) annotation, coexpression network and qRT-PCR tests revealed that these CsNAC genes may simultaneously regulate dimorphic floret development and the response to stress. Our results may help to characterize the NAC transcription factors in C. songorica and provide new insights into the functional research and application of the NAC family in crop improvement, especially in dimorphic floret plants.

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“…After the release of the Chinese white pear genome sequencing data, there were many TF genes at the whole-genome level have been identified and characterized, including NAC-TF, BAM-TF and WRKY-TF et.al. [22,46,47]. bHLH transcription factors are involved in many pathways in plant growth and metabolism [12].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide Identification of PbrbHLH Family Genes, and Expression Analysis in Response to drought and Cold Stresses in Pear (Pyrus Bretschneideri)

Dong

Chen

Dai

et al. 2020

Preprint

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Background: The basic helix-loop-helix (bHLH) transcription factors play important roles in many processes in plant growth, metabolism and responses to abiotic stresses. Although, the sequence of Chinese white pear genome (cv. ‘Dangshansuli’) has already been reported, there is still a lack of clarity regarding the bHLH family genes and their evolutionary history. Results: In this work, a genome-wide identification of the bHLH genes in Chinese white pear was performed, and we characterized the functional roles of these PbrbHLH genes in response to abiotic stresses. Based on the phylogenetic analysis and structural characteristics, 197 identified bHLH genes could be well classified into 21 groups. Expansion of PbrbHLH gene family were mainly driven by WGD and dispersed duplication with the purifying selection from the recent WGD. The functional annotation enrichment showed that the majority of PbrbHLHs were enriched in the GO terms and KEGG pathways involved in responds to stress conditions as TFs. Transcriptomic profiles and qRT-PCR revealed that PbrbHLH7, PbrbHLH8, PbrbHLH116, PbrbHLH128, PbrbHLH160 and PbrbHLH195 were significantly up-regulated under cold and drought treatments. In addition, PbrbHLH195-silenced pear seedlings display significant reduced cold tolerance, exhibiting reduced chlorophyll content, as well as increased Electrolyte leakage and concentrations of malondialdehyde and H2O2.Conclusion: For the first time, a comprehensive analysis identified the bHLH genes in Chinese white pear and demonstrated that PbrbHLH195 is involved in the production of ROS in response to cold stress, suggesting that members of the PbrbHLH family play an essential role in the stress tolerance of pear.

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Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)

Cited by 53 publications

References 96 publications

Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Genome-Wide Analysis of the Role of NAC Family in Flower Development and Abiotic Stress Responses in Cleistogenes songorica

Genome-wide Identification of PbrbHLH Family Genes, and Expression Analysis in Response to drought and Cold Stresses in Pear (Pyrus Bretschneideri)

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