scholarly journals Genome-wide identification and characterization of the CLASP_N gene family in upland cotton (Gossypium hirsutum L.)

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12733
Author(s):  
Meijun Ji ◽  
Kangtai Sun ◽  
Hui Fang ◽  
Zhimin Zhuang ◽  
Haodong Chen ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Pattern ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Evolutionary Process ◽  
Fiber Development ◽  
Family Characteristics ◽  
Evolutionary Analysis ◽  
Qrt Pcr ◽  
Genome Wide

Background Cytoplasmic linker–associated proteins (CLASPs) are tubule proteins that can bind to microtubules and participate in regulating the structure and function of microtubules, which significantly affects the development and growth of plants. These proteins have been identified in Arabidopsis; however, little research has been performed in upland cotton. Methods In this study, the whole genome of the CLASP_N family was analyzed to provide theoretical support for the function of this gene family in the development of upland cotton fiber. Bioinformatics was used to analyze the family characteristics of CLASP_N in upland cotton, such as member identification, sequence characteristics, conserved domain structure and coevolutionary relationships. Real-time fluorescent quantitative PCR (qRT-PCR) was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber. Results At the genome-wide level, we identified 16 upland cotton CLASP_N genes. A chromosomal localization analysis revealed that these 16 genes were located on 13 chromosomes. The motif results showed that all CLASP_N proteins have the CLASP_N domain. Gene structure analysis showed that the structure and length of exons and introns were consistent in the subgroups. In the evolutionary analysis with other species, the gene family clearly diverged from the other species in the evolutionary process. A promoter sequence analysis showed that this gene family contains a large number of cis-acting elements related to a variety of plant hormones. qRT-PCR was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber and leaves, and Gh210800 was found to be highly expressed in the later stages of fiber development. The results of this study provide a foundation for further research on the molecular role of the CLASP_N genes in cotton fiber development.

scholarly journals Identification of TPX2 Gene Family in Upland Cotton and Its Functional Analysis in Cotton Fiber Development

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 508 ◽  
Author(s):  
Lei ◽  
Liu ◽  
Fan ◽  
Peng ◽  
Zou ◽  
...  
Keyword(s):  
Gene Family ◽  
Upland Cotton ◽  
Recombinant Inbred Lines ◽  
Fiber Quality ◽  
Fiber Development ◽  
Microtubule Depolymerization ◽  
Genome Wide ◽  
A Genome ◽  
Associated Proteins ◽  
Tubulin Protein

Microtubules (MTs) are of importance to fiber development. The Xklp2 (TPX2) proteins as a class of microtubule-associated proteins (MAPs) play a key role in plant growth and development by regulating the dynamic changes of microtubules (MTs). However, the mechanism underlying this is unknown. The interactions between TPX2 proteins and tubulin protein, which are the main structural components, have not been studied in fiber development of upland cotton. Therefore, a genome-wide analysis of the TPX2 family was firstly performed in Gossypium hirsutum L. This study identified 41 GhTPX2 sequences in the assembled G. hirsutum genome by a series of bioinformatic methods. Generally, this gene family is phylogenetically grouped into six subfamilies, and 41 G. hirsutum TPX2 genes (GhTPX2s) are distributed across 21 chromosomes. A heatmap of the TPX2 gene family showed that homologous GhTPX2 genes, GhWDLA2/7 and GhWDLA4/9, have large differences in expression levels between two upland cotton recombinant inbred lines (69307 and 69362) that are different in fiber quality at 15 and 20 days post anthesis. The relative data indicate that these four genes are down-regulated under oryzalin, which causes microtubule depolymerization, as determined via qRT-PCR. A subcellular localization experiment suggested that GhWDLA2 and GhWDLA7 are localized to the microtubule cytoskeleton, and GhWDLA4 and GhWDLA9 are only localized to the nucleus. However, only GhWDLA7 between GhWDLA2 and GhWDLA7 interacted with GhTUA2 in the yeast two-hybrid assay. These results lay the foundation for further function study of the TPX2 gene family.

scholarly journals Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

2021 ◽  
Author(s):  
Yongxian Tian ◽  
Qigang Wang ◽  
Hao Zhang ◽  
Ningning Zhou ◽  
Huijun Yan ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
Mlo Gene Family

scholarly journals Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 128 ◽  
Author(s):  
Haron Salih ◽  
Shoupu He ◽  
Hongge Li ◽  
Zhen Peng ◽  
Xiongming Du
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Cotton Fiber ◽  
Metabolic Pathways ◽  
Higher Plants ◽  
Fiber Development ◽  
Protein Family ◽  
Sequencing Analysis ◽  
Cotton Fiber Development ◽  
Cotton Species

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.

scholarly journals Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiang Ma ◽  
Nuohan Wang ◽  
Pengbo Hao ◽  
Huiru Sun ◽  
Congcong Wang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cotton Fiber ◽  
Secondary Cell Wall ◽  
Fiber Strength ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Regulatory Relationship ◽  
Genome Wide ◽  
Regulation Functions

Abstract Background Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.). Results In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers. Conclusion We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.

scholarly journals Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Zhaoen Yang ◽  
Qian Gong ◽  
Wenqiang Qin ◽  
Zuoren Yang ◽  
Yuan Cheng ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Upland Cotton ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Wox Genes
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