scholarly journals Genome-wide investigation of heat shock transcription factor family in wheat (Triticum aestivum L.)

2019 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Sha Li ◽  
Wei Li ◽  
Qi Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Reference Genome ◽  
Phylogenetic Analyses ◽  
Triticum Aestivum L ◽  
Growth Stages ◽  
Rna Seq ◽  
Male Sterile ◽  
Heat Shock Transcription Factors ◽  
Genome Wide ◽  
Resistance To Heat

Abstract Background: Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Investigating the HSF family is essential for understanding the fertility conversion mechanism in thermo-sensitive male sterile wheat. Previous studies have investigated the HSF family in wheat but it is necessary to conduct more in-depth and systematic analyses based on the newly published reference genome. Results: In the present study, 61 wheat Hsf (TaHsf) genes were identified using two main strategies and renamed based on their physical locations on chromosomes. According to the gene structure and phylogenetic analyses, the 61 TaHsf genes were classified into three categories and eleven subclasses. The genes were unequally distributed on 21 chromosomes, including two pairs of tandem duplication genes and 52 TaHsf segmental duplication genes. According to the cis-elements identified, most of the TaHsfs can be activated by Ca++ and MYB, and they respond to drought, light, copper, and other stresses as well as heat shock. RNA-seq analysis indicated that the A2 class TaHsf genes exhibited persistently upregulated expression levels in the leaves/shoots, roots (except in the vegetative growth and reproductive growth stages), spikes, and grains in wheat under normal conditions. The A and B class TaHsf genes were positively regulated during the resistance to heat, whereas the C class genes were involved in drought regulation in wheat. Only the A and B class TaHsf genes were upregulated under fertile conditions in thermo-sensitive male sterile wheat. Conclusion: In this study, 61 wheat Hsf genes were identified based on the complete wheat reference genome. This comprehensive analysis provides novel insights into the TaHsf genes, including their diverse functions and involvement in metabolic pathways.

scholarly journals Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat (Triticum aestivum L.) and Possible Roles in Anther Development

2020 ◽  
Vol 21 (2) ◽  
pp. 608 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Gan Hu ◽  
Qi Liu ◽  
Wei Li ◽  
...  
Keyword(s):  
Heat Shock ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Heat Shock Protein 90 ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Anther Development ◽  
Male Sterile ◽  
Specific Expression ◽  
Genome Wide

Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Recently, HSFs have been shown to play roles in anther development. Thus, investigating the HSF family members and identifying their protective roles in anthers are essential for the further development of male sterile wheat breeding. In the present study, 61 wheat HSF genes (TaHsfs) were identified in the whole wheat genome and they are unequally distributed on 21 chromosomes. According to gene structure and phylogenetic analyses, the 61 TaHsfs were classified into three categories and 12 subclasses. Genome-wide duplication was identified as the main source of the expansion of the wheat HSF gene family based on 14 pairs of homeologous triplets, whereas only a very small number of TaHsfs were derived by segmental duplication and tandem duplication. Heat shock protein 90 (HSP90), HSP70, and another class of chaperone protein called htpG were identified as proteins that interact with wheat HSFs. RNA-seq analysis indicated that TaHsfs have obvious period- and tissue-specific expression patterns, and the TaHsfs in classes A and B respond to heat shock, whereas the C class TaHsfs are involved in drought regulation. qRT-PCR identified three TaHsfA2bs with differential expression in sterile and fertile anthers, and they may be candidate genes involved in anther development. This comprehensive analysis provides novel insights into TaHsfs, and it will be useful for understanding the mechanism of plant fertility conversion.

scholarly journals Genome-Wide Identification and Characterization of Heat-Shock Transcription Factors in Rubber Tree

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1157 ◽  
Author(s):  
Yan Li ◽  
Wencai Yu ◽  
Yueyi Chen ◽  
Shuguang Yang ◽  
Shaohua Wu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Cold Stress ◽  
Expression Patterns ◽  
Rubber Tree ◽  
Protein Motifs ◽  
Heat Shock Transcription Factors ◽  
Genome Wide ◽  
Cold Tolerant ◽  
Oligomerization Domain

Heat-shock transcription factors (Hsfs) play a pivotal role in the response of plants to various stresses. The present study aimed to characterize the Hsf genes in the rubber tree, a primary global source of natural rubber. In this study, 30 Hsf genes were identified in the rubber tree using genome-wide analysis. They possessed a structurally conserved DNA-binding domain and an oligomerization domain. On the basis of the length of the insert region between HR-A and HR-B in the oligomerization domain, the 30 members were clustered into three classes, Classes A (18), B (10), and C (2). Members within the same class shared highly conserved gene structures and protein motifs. The background expression levels of 11 genes in cold-tolerant rubber-tree clone 93-14 were significantly higher than those in cold-sensitive rubber-tree clone Reken501, while four genes exhibited inverse expression patterns. Upon cold stress, 20 genes were significantly upregulated in 93-114. Of the upregulated genes, HbHsfA2b, HbHsfA3a, and HbHsfA7a were also significantly upregulated in three other cold-tolerant rubber-tree clones at one or more time intervals upon cold stress. Their nuclear localization was verified, and the protein–protein interaction network was predicted. This study provides a basis for dissecting Hsf function in the enhanced cold tolerance of the rubber tree.

Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula

2011 ◽  
Vol 39 (2) ◽  
pp. 1877-1886 ◽  
Author(s):  
Fangming Wang ◽  
Qing Dong ◽  
Haiyang Jiang ◽  
Suwen Zhu ◽  
Beijiu Chen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Medicago Truncatula ◽  
Populus Trichocarpa ◽  
Heat Shock Transcription Factors ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Comprehensive analysis of polygalacturonase family highlights candidate genes related to pollen development and male fertility in wheat (Triticum aestivum L.)

2019 ◽  
Author(s):  
Jiali Ye ◽  
Xuetong Yang ◽  
Zhiquan Yang ◽  
Wei Li ◽  
Qi Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Candidate Genes ◽  
Pollen Development ◽  
Male Fertility ◽  
Triticum Aestivum L ◽  
Segmental Duplications ◽  
Rna Seq ◽  
Male Sterile ◽  
Wide Range

Abstract Background: Polygalacturonase (PG) belongs to a large family of hydrolases with important functions in cell separation during plant growth and development via the degradation of pectin. The specific expression of PG genes in anthers may be significant for male sterility research and hybrid wheat breeding, but it has not been characterized in wheat (Triticum aestivum L.). Results: We systematically studied the PG gene family using the latest published wheat reference genomic information. In total, 113 wheat PG genes were identified and renamed as TaPG01–113 based on their chromosomal positions. The PG genes are unequally distributed on 21 chromosomes and classified according to six categories from A–F. Analysis of the gene structures and conserved motifs demonstrated that the Class C and D TaPGs have relatively short gene sequences and a small number of introns. Class E TaPGs are the least conserved and lack conserved domain III. Polyploidy and segmental duplications in wheat were mainly responsible for the expansion of the wheat PG gene family. Predictions of cis-elements indicate that TaPGs have a wide range of functions, including the responses to light, hypothermia, anaerobic conditions, and hormonal stimulation, as well as being involved in meristematic tissue expression. RNA-seq showed that TaPGs have specific temporal and spatial expression characteristics. Twelve spike-specific TaPGs were screened using RNA-seq data and verified by qRT-PCR in the sterile and fertile anthers of thermo-sensitive male-sterile wheat. Four important candidate genes were identified as involved in the male fertility determination process. In fertile anthers, TaPG09 may be involved in the separation of pollen. TaPG87 and TaPG95 could play important roles in anther dehiscence. TaPG93 may be related to pollen development and pollen tube elongation. Conclusions: We analyzed the wheat PG gene family and identified four important TaPGs with differential expression levels in the wheat fertility conversion process. Our findings may facilitate functional investigations of the wheat PG gene family and provide new insights into the fertility conversion mechanism in male-sterile wheat.

scholarly journals Genome-wide Scanning and Characterization of Sorghum bicolor L. Heat Shock Transcription Factors

2015 ◽  
Vol 16 (4) ◽  
pp. 279-291 ◽  
Author(s):  
M. Nagaraju ◽  
Palakolanu Sudhakar Reddy ◽  
S. Anil Kumar ◽  
Rakesh K. Srivastava ◽  
P. B. Kavi Kishor ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Heat Shock ◽  
Sorghum Bicolor ◽  
Heat Shock Transcription Factors ◽  
Genome Wide ◽  
Sorghum Bicolor L

scholarly journals Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3747 ◽  
Author(s):  
Weilong Kong ◽  
Shaozong Yang ◽  
Yulu Wang ◽  
Mohammed Bendahmane ◽  
Xiaopeng Fu
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Growth And Development ◽  
Phylogenetic Analyses ◽  
Rna Seq ◽  
Reference Base ◽  
Genome Wide ◽  
Aquaporin Gene ◽  
Identification And Characterization

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

scholarly journals The genome sequence of Sorbus pohuashanensis provides insights into population evolution and leaf sunburn response

2021 ◽  
Author(s):  
Dongxue Zhao ◽  
Yan Zhang ◽  
Yizeng Lu ◽  
Mao Chai ◽  
Liqiang Fan ◽  
...  
Keyword(s):  
Heat Shock ◽  
Reference Genome ◽  
De Novo ◽  
Leaf Shape ◽  
Gene Families ◽  
Natural Hybridization ◽  
Rna Seq ◽  
Long Reads ◽  
High Level ◽  
Chromosomal Synteny

Sorbus pohuashanensis is a potential horticulture and medicinal plant, but its genomic and genetic background remains unknown. Here, we de novo sequenced and assembled the S. pohuashanensis (Hance) Hedl. reference genome using PacBio long reads. Based on the new reference genome, we resequenced a core collection of 22 Sorbus spp. samples, which were divided into two groups (G1 and G2) based on phylogenetic and PCA analysis. These phylogenetic clusters were highly in accordance with the classification based on leaf shape. Natural hybridization between the G1 and G2 groups was evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis showed that G1 has a higher diversity than G2, and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and gene families involved in energy consumption contracted. Comparative genome analysis showed that S. pohuashanensis has a high level of chromosomal synteny with Malus domestica and Pyrus communis. RNA-seq data suggested that flavonol biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This research provides new insight into the evolution of Sorbus spp. genomes. In addition, the genomic resources and the identified genetic variations, especially those genes related to stress resistance, will help future efforts to introduce and breed Sorbus spp.

Sign in / Sign up

Export Citation Format

Share Document