scholarly journals Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Roshan Zameer ◽  
Muhammad Sadaqat ◽  
Kinza Fatima ◽  
Sajid Fiaz ◽  
Sumaira Rasul ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Nuclear Genome ◽  
Functional Study ◽  
Promoter Sequences ◽  
Physiological Processes ◽  
Genome Wide ◽  
Two Component ◽  
Two Component Signal Transduction ◽  
Drought And Salt Stresses ◽  
As Stress

The two-component signal transduction system (TCS) acts in a variety of physiological processes in lower organisms and has emerged as a key signaling system in both prokaryotes and eukaryotes, including plants. TCS genes assist plants in processes such as stress resistance, cell division, nutrition signaling, leaf senescence, and chloroplast division. In plants, this system is composed of three types of proteins: response regulators (RRs), histidine kinases (HKs), and histidine phosphotransfer proteins (HPs). We aimed to study the Sorghum bicolor genome and identified 37 SbTCS genes consisting of 13 HKs, 5 HPs, and 19 RRs (3 type-A RRs, 7 type-B RRs, 2 type-C RRs, and 7 pseudo-RRs). The structural and phylogenetic comparison of the SbTCS members with their counterparts in Arabidopsis thaliana, Oryza sativa, Cicer arietinum, and Glycine max showed group-specific conservations and variations. Expansion of the gene family members is mostly a result of gene duplication, of both the tandem and segmental types. HKs and RRs were observed to be originated from segmental duplication, while some HPs originated from tandem duplication. The nuclear genome of S. bicolor contain 10 chromosomes and these SbTCS genes are randomly distributed on all the chromosomes. The promoter sequences of the SbTCS genes contain several abiotic stress-related cis-elements. RNA-seq and qRT-PCR-based expression analysis demonstrated most of the TCS genes were responsive to drought and salt stresses in leaves, which suggest their role in leaf development. This study lays a foundation for further functional study of TCS genes for stress tolerance and developmental improvement in S. bicolor.

scholarly journals Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

2021 ◽  
Vol 22 (16) ◽  
pp. 8748
Author(s):  
Longjie Ni ◽  
Zhiquan Wang ◽  
Zekai Fu ◽  
Dina Liu ◽  
Yunlong Yin ◽  
...  
Keyword(s):  
Stress Responses ◽  
Growth And Development ◽  
Cis Elements ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Drought And Salt Stresses ◽  
Salt And Drought Stress ◽  
As Stress ◽  
Bhlh Proteins

The basic helix-loop-helix (bHLH) family of transcription factors is one of the most significant and biggest in plants. It is involved in the regulation of both growth and development, as well as stress response. Numerous members of the bHLH family have been found and characterized in woody plants in recent years. However, no systematic study of the bHLH gene family has been published for Hibiscus hamabo Sieb. et Zucc. In this research, we identified 162 bHLH proteins (HhbHLHs) from the genomic and transcriptomic datasets of H. hamabo, which were phylogenetically divided into 19 subfamilies. According to a gene structural study, the number of exon-introns in HhbHLHs varied between zero and seventeen. MEME research revealed that the majority of HhbHLH proteins contained three conserved motifs, 1, 4, and 5. The examination of promoter cis-elements revealed that the majority of HhbHLH genes had several cis-elements involved in plant growth and development and abiotic stress responses. In addition, the overexpression of HhbHLH2 increased salt and drought stress tolerance in Arabidopsis.

scholarly journals Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Stéphanie Borland ◽  
Anne Oudart ◽  
Claire Prigent-Combaret ◽  
Céline Brochier-Armanet ◽  
Florence Wisniewski-Dyé
Keyword(s):  
Signal Transduction ◽  
Plant Growth ◽  
Genome Wide ◽  
Two Component ◽  
Plant Growth Promoting ◽  
Two Component Signal Transduction ◽  
Growth Promoting ◽  
Genome Wide Survey ◽  
Signal Transduction Systems

scholarly journals Genome-Wide Identification of Two-Component Signal Transduction System Genes in Melon (<I>Cucumis melon</I> L.)

2018 ◽  
Vol 09 (04) ◽  
pp. 469-479 ◽  
Author(s):  
Panjing Liu ◽  
Xiaoyu Yang ◽  
Yana Zhang ◽  
Shuoshuo Wang ◽  
Qian Ge ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Signal Transduction System ◽  
Genome Wide ◽  
Two Component ◽  
Two Component Signal Transduction

scholarly journals Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Fan ◽  
Jun Yan ◽  
Dili Lai ◽  
Hao Yang ◽  
Guoxing Xue ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Sorghum Bicolor ◽  
Plant Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Tandem Repeats ◽  
Functional Study ◽  
Systematic Analysis ◽  
Genome Wide ◽  
The Relationship

Abstract Background GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. Results A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. Conclusions Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor.

scholarly journals Nuclear genome-wide associations with mitochondrial heteroplasmy

2021 ◽  
Vol 7 (12) ◽  
pp. eabe7520
Author(s):  
Priyanka Nandakumar ◽  
Chao Tian ◽  
Jared O’Connell ◽  
David Hinds ◽  
Andrew D. Paterson ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Multiple Roles ◽  
European Ancestry ◽  
Mitochondrial Transcription Factor ◽  
Genome Wide ◽  
Mtdna Sequence ◽  
Nuclear Component ◽  
Mitochondrial Transcription Factor A ◽  
Mitochondrial Heteroplasmy ◽  
The Stability

The role of the nuclear genome in maintaining the stability of the mitochondrial genome (mtDNA) is incompletely known. mtDNA sequence variants can exist in a state of heteroplasmy, which denotes the coexistence of organellar genomes with different sequences. Heteroplasmic variants that impair mitochondrial capacity cause disease, and the state of heteroplasmy itself is deleterious. However, mitochondrial heteroplasmy may provide an intermediate state in the emergence of novel mitochondrial haplogroups. We used genome-wide genotyping data from 982,072 European ancestry individuals to evaluate variation in mitochondrial heteroplasmy and to identify the regions of the nuclear genome that affect it. Age, sex, and mitochondrial haplogroup were associated with the extent of heteroplasmy. GWAS identified 20 loci for heteroplasmy that exceeded genome-wide significance. This included a region overlapping mitochondrial transcription factor A (TFAM), which has multiple roles in mtDNA packaging, replication, and transcription. These results show that mitochondrial heteroplasmy has a heritable nuclear component.

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