Genome-Wide Identification of Papain-Like Cysteine Proteases in Gossypium hirsutum and Functional Characterization in Response to Verticillium dahliae

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

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GhKWL1 Upregulates GhERF105 but Its Function Is Impaired by Binding with VdISC1, a Pathogenic Effector of Verticillium dahliae

International Journal of Molecular Sciences ◽

10.3390/ijms22147328 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7328

Author(s):

Yang Chen ◽

Mi Zhang ◽

Lei Wang ◽

Xiaohan Yu ◽

Xianbi Li ◽

...

Keyword(s):

Gene Expression ◽

Transgenic Plants ◽

Gossypium Hirsutum ◽

Verticillium Wilt ◽

Verticillium Dahliae ◽

Defense Response ◽

Upland Cotton ◽

Effector Protein ◽

Positive Regulator ◽

Its Gene

Verticillium wilt, caused by Verticillium dahliae, is a devastating disease for many important crops, including cotton. Kiwellins (KWLs), a group of cysteine-rich proteins synthesized in many plants, have been shown to be involved in response to various phytopathogens. To evaluate genes for their function in resistance to Verticillium wilt, we investigated KWL homologs in cotton. Thirty-five KWL genes (GhKWLs) were identified from the genome of upland cotton (Gossypium hirsutum). Among them, GhKWL1 was shown to be localized in nucleus and cytosol, and its gene expression is induced by the infection of V. dahliae. We revealed that GhKWL1 was a positive regulator of GhERF105. Silencing of GhKWL1 resulted in a decrease, whereas overexpression led to an increase in resistance of transgenic plants to Verticillium wilt. Interestingly, through binding to GhKWL1, the pathogenic effector protein VdISC1 produced by V. dahliae could impair the defense response mediated by GhKWL1. Therefore, our study suggests there is a GhKWL1-mediated defense response in cotton, which can be hijacked by V. dahliae through the interaction of VdISC1 with GhKWL1.

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Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Journal of Cotton Research ◽

10.1186/s42397-021-00090-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Teame Gereziher MEHARI ◽

Yanchao XU ◽

Richard Odongo MAGWANGA ◽

Muhammad Jawad UMER ◽

Joy Nyangasi KIRUNGU ◽

...

Keyword(s):

Drought Stress ◽

Gossypium Hirsutum ◽

Abiotic Stresses ◽

Substitution Rate ◽

Synonymous Substitution ◽

Synonymous Substitution Rate ◽

Drought Tolerant ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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Genome-Wide Mining of MYB Transcription Factors in the Anthocyanin Biosynthesis Pathway of Gossypium Hirsutum

Biochemical Genetics ◽

10.1007/s10528-021-10027-0 ◽

2021 ◽

Author(s):

Yingjie Zhu ◽

Ying Bao

Keyword(s):

Transcription Factors ◽

Gossypium Hirsutum ◽

Anthocyanin Biosynthesis ◽

Biosynthesis Pathway ◽

Myb Transcription Factors ◽

Genome Wide

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Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

Evolutionary Bioinformatics ◽

10.1177/1176934319889948 ◽

2019 ◽

Vol 15 ◽

pp. 117693431988994

Author(s):

Shulin Zhang ◽

Yaling Cai ◽

Jinggong Guo ◽

Kun Li ◽

Renhai Peng ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Genetic Relationships ◽

Phylogenetic Analyses ◽

Genotyping By Sequencing ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Breeding Programs ◽

Association Analyses ◽

Genome Wide ◽

Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

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Genetics and Epigenetics of Atrial Fibrillation

International Journal of Molecular Sciences ◽

10.3390/ijms21165717 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5717 ◽

Cited By ~ 1

Author(s):

Estefanía Lozano-Velasco ◽

Diego Franco ◽

Amelia Aranega ◽

Houria Daimi

Keyword(s):

Atrial Fibrillation ◽

Regulatory Networks ◽

Association Studies ◽

Functional Characterization ◽

The Elderly ◽

Supraventricular Arrhythmia ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Transcriptional Regulatory ◽

Transcriptional Regulatory Mechanisms

Atrial fibrillation (AF) is known to be the most common supraventricular arrhythmia affecting up to 1% of the general population. Its prevalence exponentially increases with age and could reach up to 8% in the elderly population. The management of AF is a complex issue that is addressed by extensive ongoing basic and clinical research. AF centers around different types of disturbances, including ion channel dysfunction, Ca2+-handling abnormalities, and structural remodeling. Genome-wide association studies (GWAS) have uncovered over 100 genetic loci associated with AF. Most of these loci point to ion channels, distinct cardiac-enriched transcription factors, as well as to other regulatory genes. Recently, the discovery of post-transcriptional regulatory mechanisms, involving non-coding RNAs (especially microRNAs), DNA methylation, and histone modification, has allowed to decipher how a normal heart develops and which modifications are involved in reshaping the processes leading to arrhythmias. This review aims to provide a current state of the field regarding the identification and functional characterization of AF-related epigenetic regulatory networks

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