A Genome-Scale Analysis of the PIN Gene Family Reveals Its Functions in Cotton Fiber Development

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.

Download Full-text

Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

10.21203/rs.2.21774/v2 ◽

2020 ◽

Author(s):

Qun Ge(Former Corresponding Author) ◽

Yànli Cūi ◽

Jùnwén Lǐ ◽

Jǔwǔ Gōng ◽

Quánwěi Lú ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Cotton Fiber ◽

Calvin Cycle ◽

Purifying Selection ◽

Fiber Development ◽

Plant Responses ◽

Cotton Fiber Development ◽

Systemic Analysis ◽

Fructose 1,6 Bisphosphatase

Abstract Background: Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species.Results: A total of 41 FBP genes from four Gossypium species were identified and analyzed. These FBP genes were sorted into two groups and seven subgroups. Results revealed that FBP family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in a translocated DNA fragment and the whole FBP gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in G. barbadense and in At subgenome than those in other Gossypium species and in the Dt subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different FBP genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to Verticillium wilt onset (two genes) and to salt stress (eight genes).Conclusion: The FBP gene family displayed a disequilibrium evolution pattern in Gossypium species, which led to diversified functions affecting not only fiber development, but also responses to Verticillium wilt and salt stress. All of these findings provide the foundation for further study of the function of FBP genes in cotton fiber development and in environmental adaptability.

Download Full-text

Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

Journal of Cotton Research ◽

10.1186/s42397-021-00099-z ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Senmiao FAN ◽

Aiying LIU ◽

Xianyan ZOU ◽

Zhen ZHANG ◽

Qun GE ◽

...

Keyword(s):

Gene Family ◽

Cotton Fiber ◽

Fiber Strength ◽

Expression Patterns ◽

Fiber Development ◽

Fiber Elongation ◽

Transcript Levels ◽

Cotton Fiber Development ◽

Conserved Sequence ◽

Cotton Species

Abstract Background Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTs has not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development. Results In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondii, G. barbadense, G. hirsutum, and G. arboreum), and classified them as GAUT-A, GAUT-B and GAUT-C, which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis-elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development. Conclusions The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.

Download Full-text

Disequilibrium evolution of Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

10.21203/rs.2.21774/v1 ◽

2020 ◽

Author(s):

Qun Ge ◽

Yànli Cūi ◽

Jùnwén Lǐ ◽

Jǔwǔ Gōng ◽

Quánwěi Lú ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Cotton Fiber ◽

Calvin Cycle ◽

Purifying Selection ◽

Fiber Development ◽

Plant Responses ◽

Cotton Fiber Development ◽

Evolution Pattern ◽

Fructose 1,6 Bisphosphatase

Abstract Background：Fructose-1,6-bisphosphatase (FBP) is a key enzyme in plant sucrose synthesis pathway in Calvin cycle and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of the FBPs has been reported in Gossypium species.Results：A total of 41 FBP genes from four Gossypium species were identified and analyzed. The FBP genes were assorted into two groups and 7 subgroups. The results revealed that FBP family genes were under a purifying selection pressure which rendered FBP family members a conserved evolution pattern and that there was no tandem and fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in the translocated DNA fragment and the whole FBP gene family was under a disequilibrium evolution pattern which led to a faster evolution progress of the members in G. barbadense and in At subgenome than those in the rest Gossypium species and in Dt subgenome, respectively of this study. Through RNA-seq analyses and qRT-PCR verifications, different FBP genes have diversified biological functions in cotton fiber development (2 genes in 0 DPA and 1DPA ovules and 4 genes in 20-25 DPA fibers), and in plant responses to Verticillium wilt onset (2 genes) and to salt stress (8 genes).Conclusion: The FBP gene family displayed disequilibrium evolution pattern in Gossypium species, which render them diversified functions affecting not only fiber development, but also responses to the Verticillium wilt and the salt stress. All the findings provided the foundation for further study of the function of the FBP genes in cotton fiber development and in environmental adaptability.

Download Full-text

Disequilibrium evolution of Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

10.21203/rs.2.21774/v3 ◽

2020 ◽

Author(s):

Qun Ge ◽

Yànli Cūi ◽

Jùnwén Lǐ ◽

Jǔwǔ Gōng ◽

Quánwěi Lú ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Cotton Fiber ◽

Calvin Cycle ◽

Purifying Selection ◽

Fiber Development ◽

Plant Responses ◽

Cotton Fiber Development ◽

Systemic Analysis ◽

Fructose 1,6 Bisphosphatase

Abstract Background: Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species.Results: A total of 41 FBP genes from four Gossypium species were identified and analyzed. These FBP genes were sorted into two groups and seven subgroups. Results revealed that FBP family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in a translocated DNA fragment and the whole FBP gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in G. barbadense and in At subgenome than those in other Gossypium species and in the Dt subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different FBP genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to Verticillium wilt onset (two genes) and to salt stress (eight genes).Conclusion: The FBP gene family displayed a disequilibrium evolution pattern in Gossypium species, which led to diversified functions affecting not only fiber development, but also responses to Verticillium wilt and salt stress. All of these findings provide the foundation for further study of the function of FBP genes in cotton fiber development and in environmental adaptability.

Download Full-text

Evolution of pectin-synthesis-relevant galacturonosyltransferase gene family and its expression during cotton fiber development

10.21203/rs.3.rs-152342/v1 ◽

2021 ◽

Author(s):

FAN Senmiao ◽

LIU Aiying ◽

ZOU Xianyan ◽

ZHANG Zhen ◽

GE Qun ◽

...

Keyword(s):

Gene Family ◽

Cotton Fiber ◽

Fiber Strength ◽

Expression Patterns ◽

Major Effect ◽

Fiber Development ◽

Future Research ◽

Fiber Elongation ◽

Cotton Fiber Development ◽

Cotton Species

Abstract Background: Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTs has not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development.Results: In this study, we identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondii, G. barbadense, G. hirsutum, and G. arboreum), and classified them as GAUT-A, GAUT-B and GAUT-C. Among them, 15 GAUT genes encoded proteins (GAUT1 to GAUT15). All GAUT family genes except for the gene GAUT7 coding contained a consevrved Glyco_transf_8 domain (H-DN-A-SVV-S-V-H-T-F). The consevrved sequences of GAUT7 was a PLN (phospholamban) 02769 domain, categorized as a probable galacturonosyltransferase. According to cis-elemet analysis, GAUT genes expression may be regulated by hormones such as JA, GA, SA, ABA, Me-JA and IAA. The evolution and expression patterns of the GAUT gene family in different cotton species and the expression levels in upland cotton materials having different fiber strengths were analyzed. Peak expression of GhGAUT genes was observed before 15DPA; in the six materials with high fiber strength, the expression was concentrated from 10 to 15DPA; while the highest expression in low fiber strength materials was detected between 5 and 10 DPA. The results presented in this paper lays the foundation for future research on gene function during cotton fiber development.Conclusions: The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low-strength-fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high-strength fiber is related to both elongation and thickening.

Download Full-text