Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species

Fan, Kai; Mao, Zhijun; Ye, Fangting; Pan, Xinfeng; Li, Zhaowei; Lin, Weiwei; Zhang, Yongqiang; Huang, Jinwen

doi:10.1016/j.ygeno.2021.07.008

Cited by 16 publications

(9 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Investigating the origin and differentiation of gene families is a prime research focus of evolutionary studies. Identifying a gene family based on the whole genome data is of great significance for understanding gene evolution history, gene function and species differentiation [57,58]. According to the phylogenetic tree analysis of NAC genes in J. mandshurica and A. thaliana, 114 JmNACs were significantly clustered into eight subgroups (Figure 2), wherein Group I contained the largest number of JmNAC and AtNAC genes, and the genes from Group I mainly involved in DNA-binding TF activity, embryo development, leaf senescence, signal transduction, oxidative stress response, and xylem formation, indicating various functions of JmNAC genes in plant growth and development as well as stress response.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

Cai

Pei

et al. 2021

IJMS

View full text Add to dashboard Cite

The NAC (NAM, ATAF and CUC) gene family plays a crucial role in the transcriptional regulation of various biological processes and has been identified and characterized in multiple plant species. However, genome-wide identification of this gene family has not been implemented in Juglans mandshurica, and specific functions of these genes in the development of fruits remain unknown. In this study, we performed genome-wide identification and functional analysis of the NAC gene family during fruit development and identified a total of 114 JmNAC genes in the J. mandshurica genome. Chromosomal location analysis revealed that JmNAC genes were unevenly distributed in 16 chromosomes; the highest numbers were found in chromosomes 2 and 4. Furthermore, according to the homologues of JmNAC genes in Arabidopsis thaliana, a phylogenetic tree was constructed, and the results demonstrated 114 JmNAC genes, which were divided into eight subgroups. Four JmNAC gene pairs were identified as the result of tandem duplicates. Tissue-specific analysis of JmNAC genes during different developmental stages revealed that 39 and 25 JmNAC genes exhibited upregulation during the mature stage in walnut exocarp and embryos, indicating that they may serve key functions in fruit development. Furthermore, 12 upregulated JmNAC genes were common in fruit ripening stage in walnut exocarp and embryos, which demonstrated that these genes were positively correlated with fruit development in J. mandshurica. This study provides new insights into the regulatory functions of JmNAC genes during fruit development in J. mandshurica, thereby improving the understanding of characteristics and evolution of the JmNAC gene family.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

Cai

Pei

et al. 2021

IJMS

View full text Add to dashboard Cite

show abstract

“…HSF is a particular sort of transcription factor that is crucial for plants’ ability to resist diverse stressors [ 35 ]. The highly conserved plant HSF DBD is located at the N-terminal end where it is able to precisely locate and recognize the heat stress element (HSE) in the promoter of the target gene [ 36 , 37 , 38 ]. All MsHSF proteins comprised DBD with three helices and four folds, according to multiple sequence alignment and secondary structure prediction ( Figure 2 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of HSF Transcription Factors in Alfalfa (Medicago sativa) under Abiotic Stress

Ma¹,

Zhang²,

Ye³

et al. 2022

Plants

View full text Add to dashboard Cite

Alfalfa (Medicago sativa) is one of the most important legume forage species in the world. It is often affected by several abiotic stressors that result in reduced yields and poor growth. Therefore, it is crucial to study the resistance of M. sativa to abiotic stresses. Heat shock transcription factors (HSF) are key players in a number of transcriptional regulatory pathways. These pathways play an essential role in controlling how plants react to different abiotic stressors. Studies on the HSF gene family have been reported in many species but have not yet undergone a thorough analysis in M. sativa. Therefore, in order to identify a more comprehensive set of HSF genes, from the genomic data, we identified 16 members of the MsHSF gene, which were unevenly distributed over six chromosomes. We also looked at their gene architectures and protein motifs, and phylogenetic analysis allowed us to divide them into 3 groups with a total of 15 subgroups. Along with these aspects, we then examined the physicochemical properties, subcellular localization, synteny analysis, GO annotation and enrichment, and protein interaction networks of amino acids. Finally, the analysis of 16 MsHSF genes’ expression levels across all tissues and under four abiotic stresses using publicly available RNA-Seq data revealed that these genes had significant tissue-specific expression. Moreover, the expression of most MsHSF genes increased dramatically under abiotic stress, further validating the critical function played by the MsHSF gene family in abiotic stress. These results provided basic information about MsHSF gene family and laid a foundation for further study on the biological role of MsHSF gene in response to stress in M. sativa.

show abstract

“…All hits were further analyzed using the hmmscan program in hmmer3.0 against the local Pfam-A database to confirm a detectable HSF domain in each sequence, with a e-value setting as 0.0001. All obtained HSF candidates were validated by subjecting to the Heatster database ( Fan et al, 2021 ). Only genes simultaneously encoding DBD, HR-A and HR-B were recognized as true HSF genes, which were classified into the A, B, and C classes by the Heatster database.…”

Section: Methodsmentioning

confidence: 99%

Comparative Analysis of HSF Genes From Secale cereale and its Triticeae Relatives Reveal Ancient and Recent Gene Expansions

Feng

Zeng

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

Plants have evolved sophisticated systems to cope with the environmental stresses, with the heat shock factor (HSF) family proteins composing an integral part of the transcriptional regulation system. Understanding the evolutionary history and functional diversity of HSFs will facilitate improving tolerance of crops to adverse environmental conditions. In this study, genome-wide analysis of Secale cereale identified 31 HSF genes. The total number of HSF genes in S. cereale is larger than that in barley and the three subgenomes of wheat, suggesting it is a valuable resource for mining functional HSFs. Chromosome analysis revealed an uneven distribution of HSF genes among the 7 S. cereale chromosomes, with no HSF gene was detected on chromosome 4. Further interspecies synteny analysis revealed that chromosome reorganization during species-speciation may lead to the escape of HSF genes from the S. cereale chromosome 4. Phylogenetic analysis revealed that S. cereale experienced more HSF gene duplications than barley and the three wheat subgenomes. Expression analysis demonstrated that S. cereale HSF genes showed diverse expression patterns across plant developmental stages and upon drought and freezing treatment, suggesting functional diversity of the gene family. Notably, we detected distinct expression patterns for a recently duplicated HSF gene pair, indicating functional divergence may have occurred between the two genes. The study presents the genome organization, evolutionary features and expression patterns of the S. cereale HSF genes. These results provide new insights into the evolution of HSF genes in Triticeae and may serve as a resource for Triticeae molecular breeding.

show abstract

Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species

Cited by 16 publications

References 70 publications

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

Genome-Wide Identification of NAC Transcription Factor Family in Juglans mandshurica and Their Expression Analysis during the Fruit Development and Ripening

Genome-Wide Identification and Expression Analysis of HSF Transcription Factors in Alfalfa (Medicago sativa) under Abiotic Stress

Comparative Analysis of HSF Genes From Secale cereale and its Triticeae Relatives Reveal Ancient and Recent Gene Expansions

Contact Info

Product

Resources

About