Genome-Wide Analysis of NAC Gene Family in Betula pendula

Song, Ching; Lin, Xin; Zhang, Dawei; Li, Qi; Zhao, Xiyang; Su, Chen

doi:10.3390/f10090741

Cited by 41 publications

(53 citation statements)

References 92 publications

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“…To examine the phylogenetic relationship among VcNAC proteins, an unrooted phylogenetic tree was constructed with alignments of 158 VcNACs and 51 AtNACs. According to the structural similarity and conserved motifs, all of the NAC proteins were divided into 14 subgroups [11,35]. We found that…”

Section: Identification and Phylogenetic Analysis Of Nac Tfs In Bluebmentioning

confidence: 99%

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Liang

Wang

Sun

et al. 2019

Forests

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Research Highlights: Phenotypic changes and expression profiles, phylogeny, conserved motifs, and expression correlations of NAC (NAM, ATAF1, ATAF2 and CUC2) transcription factors (TFs) in blueberry genome were detected under drought stress, and the expression patterns and functions of 12 NACs were analyzed. Background and Objectives: Blueberry is an important shrub species with a high level of flavonoids in fruit, which are implicated in a broad range of health benefits. However, the molecular mechanism of this shrub species in response to drought stress still remains elusive. NAC TFs widely participate in stress tolerance in many plant species. The characterization and expression profiles of NAC TFs were analyzed on the basis of genome data in blueberry when subjected to drought stress. Materials and Methods: Combined with the analysis of chlorophyll a fluorescence and endogenous phytohormones, the phenotypic changes of blueberry under drought stress were observed. The phylogenetic tree, conserved motifs, differently expressed genes, and expression correlation were determined by means of multiple bioinformatics analysis. The expression profiles of NACs in different organs were examined and compared through RNA-seq and qRT-PCR assay. Results: The chlorophyll a fluorescence parameters φPo, φEo, φRo, and PIabs of leaves were significantly inhibited under drought stress. ABA (abscisic acid) content noticeably increased over the duration of drought, whereas GA3 (gibberellic acid) and IAA (indole acetic acid) content decreased continuously. A total of 158 NACs were identified in blueberry genome and 62 NACs were differently expressed in leaf and root of blueberry under drought stress. Among them, 14 NACs were significantly correlated with the expression of other NAC genes. Conclusions: Our results revealed the phenotypic changes of this shrub under drought stress and linked them with NAC TFs, which are potentially involved in the process of response to drought stress.

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Section: Identification and Phylogenetic Analysis Of Nac Tfs In Bluebmentioning

confidence: 99%

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Liang

Wang

Sun

et al. 2019

Forests

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“…In the process of genome evolution, tandem duplication and segmental duplication were the main factors that led to the expansion of gene family [35]. Certain studies have shown that tandem duplication was largely responsible for the expansion of birch gene family [33], such as tandem duplication are the main reason for the expansion of B. pendula NAC gene family [15]. By contrast, segmental duplication has contributed signi cantly to the expansion of this gene family in Pyrus bretschneideri [28].…”

Section: Discussionmentioning

confidence: 99%

“…To determine the expression patterns of BpPODs in different tissues in Betula platyphylla × Betula pendula, we downloaded the sequencing data from the NCBI SRA database with an accession number of PRJNA535361 [15]. To identify the expression of BpPODs during cold treatment in Betula platyphylla × Betula pendula, we downloaded the sequencing data from the NCBI SRA database with an accession number of PRJNA532995 [15]. The clean reads of each sample were obtained by ltering out reads of low quality.…”

Section: Differential Expression Pro Le Of Bppod Gene Familymentioning

confidence: 99%

“…The gene family always arose from multiple ways including tandem duplication, duplicative transposition, and whole genome duplication (WGD), which was followed by mutation and divergence [15]. During the last decade, several molecular biology approaches have been developed to isolate, characterize and study the expression of POD gene family in plants [6].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

Cai

Chen

Liu

et al. 2020

Preprint

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Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula , although it has been characterized in Arabidopsis , rice and maize. The POD genes remain to be determined in Betula pendula . Results : A total of 90 nonredundant POD genes were identified in Betula pendula . (designated BpPODs ). These POD genes were divided into twelve groups based on their phylogenetic relationships. The BpPODs are unevenly distributed on the 14 chromosomes. In addition, some BpPOD genes were located sequentially in tandem on chromosomes, inferred that tandem duplication contributes to the expansion of the POD genes family in Betula pendula . Analysis of the distribution of conserved domains of BpPOD proteins showed that all these proteins contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results show that some BpPOD genes might play significant roles in root, xylem, leaf and flower. Furthermore, under low temperature conditions, some BpPOD genes showed different expression patterns at different times. Conclusions: Comprehensive study of the POD genes suggests that their functional diversity during Betula pendula growth and development. Our findings provide a basis for further functional analysis on POD genes family in Betula pendula .

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“…We downloaded the transcriptome data (PRJNA535361) [18] from the NCBI SRA database to investigate the expressional patterns of B. pendula cellulose synthase genes in different tissues. The clean reads of three replicates per tissues were aligned to the B. pendula transcriptome by using STAR v2.7.3a [19], and the accurate transcript quanti cation was estimated by using RSEM v1.3.3 (RNA-seq by Expectation-Maximization) pipeline [20] with paired-end sequencing mode.…”

Section: Rna-seq Expression Analysis Of B Pendula Cell Wall Synthesimentioning

confidence: 99%

Identification of Putative Cell Wall Synthesis Genes in Betula pendula

Chen

Zhao

Chen

2020

Preprint

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Cellulose is an essential structural component of the plant cell wall and is an important resource for the production of paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues. Here we identified 46 gene models in 7 gene families which encoding cellulose synthase and related enzymes of Betula pendula , and the transcript abundance of these genes in xylem, root, leaf and flower tissues also be determined. Based on these RNA-seq data, we have identified 8 genes that most likely participate in cell wall synthesis. In parallel, a gene co-expression network was also constructed based on transcriptome sequencing.

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Genome-Wide Analysis of NAC Gene Family in Betula pendula

Cited by 41 publications

References 92 publications

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Identification and Expression of NAC Transcription Factors of Vaccinium corymbosum L. in Response to Drought Stress

Genome-Wide Identification and Analysis of Class III Peroxidases in Betula pendula

Identification of Putative Cell Wall Synthesis Genes in Betula pendula

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